graphify-labs__graphify/graphify/__main__.py

"""graphify CLI - `graphify install` sets up the Claude Code skill."""

from __future__ import annotations
import functools
import json
import os
import platform
import re
import shutil
import sys
from pathlib import Path

try:
    from importlib.metadata import version as _pkg_version

    __version__ = _pkg_version("graphifyy")
except Exception:
    __version__ = "unknown"

# Output directory — override with GRAPHIFY_OUT env var for worktrees or shared-output setups.
# Accepts a relative name ("graphify-out-feature") or an absolute path ("/shared/graphify-out").
_GRAPHIFY_OUT = os.environ.get("GRAPHIFY_OUT", "graphify-out")


@functools.lru_cache(maxsize=None)
def _always_on(basename: str) -> str:
    """Read a packaged always-on instruction block from graphify/always_on/.

    The six always-on blocks (CLAUDE.md / AGENTS.md / GEMINI.md / VS Code
    Copilot instructions / Antigravity rules / Kiro steering) live as committed
    markdown next to this module, generated by tools/skillgen from a single
    human-edited fragment and guarded against drift by ``skillgen --check``. The
    installer injects them verbatim via ``_replace_or_append_section``, so the
    bytes here must match the former triple-quoted constant exactly — the
    always-on-roundtrip validator proves that.
    """
    path = Path(__file__).parent / "always_on" / f"{basename}.md"
    try:
        return path.read_text(encoding="utf-8")
    except OSError as exc:
        # Defer to use-time so a missing/corrupt packaged block can't crash module
        # import (which would brick every CLI command, not just install). Reached
        # only by an install/integration path that actually needs this block.
        raise RuntimeError(
            f"graphify install is incomplete: missing always-on block '{basename}' "
            f"at {path}. Reinstall graphifyy (e.g. `uv tool install --reinstall graphifyy`)."
        ) from exc


_ALWAYS_ON_ALIASES = {
    "_CLAUDE_MD_SECTION": "claude-md",
    "_AGENTS_MD_SECTION": "agents-md",
    "_GEMINI_MD_SECTION": "gemini-md",
    "_VSCODE_INSTRUCTIONS_SECTION": "vscode-instructions",
    "_ANTIGRAVITY_RULES": "antigravity-rules",
    "_KIRO_STEERING": "kiro-steering",
}


def __getattr__(name: str) -> str:
    # PEP 562: lazily resolve the legacy always-on section constants for external
    # importers (e.g. the install-string tests). In-module code calls _always_on()
    # directly; nothing is read at import time, so a missing block can no longer
    # brick the CLI on `import graphify.__main__` (#1121 follow-up).
    base = _ALWAYS_ON_ALIASES.get(name)
    if base is not None:
        return _always_on(base)
    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")


def _default_graph_path() -> str:
    return str(Path(_GRAPHIFY_OUT) / "graph.json")


def _enforce_graph_size_cap_or_exit(gp: Path) -> None:
    """Reject oversized graph files before parsing (CLI exit-on-fail flavor).

    Delegates to ``graphify.security.check_graph_file_size_cap`` and turns the
    raised ``ValueError`` into a CLI-style ``error: ...`` message + exit 1.
    Use this from ``__main__.py`` subcommands that already use the ``print +
    sys.exit(1)`` idiom. Library/MCP/loader callers (``serve._load_graph``,
    ``build``, ``benchmark``, ``tree_html``, ``callflow_html``, ``prs``,
    ``global_graph``, ``watch``, ``export``) call the security helper directly
    and let the ``ValueError`` propagate.
    """
    from graphify.security import check_graph_file_size_cap
    try:
        check_graph_file_size_cap(gp)
    except ValueError as exc:
        print(f"error: {exc}", file=sys.stderr)
        sys.exit(1)


def _check_skill_version(skill_dst: Path) -> None:
    """Warn if the installed skill is from an older graphify version."""
    version_file = skill_dst.parent / ".graphify_version"
    if not version_file.exists():
        return
    if not skill_dst.exists():
        print("  warning: skill dir exists but SKILL.md is missing. Run 'graphify install' to repair.")
        return
    # A progressive SKILL.md links to its references/ sidecar. If the body points
    # at references/ but the dir is gone (manual delete, partial upgrade), the
    # on-demand fragments won't load — flag it for repair.
    try:
        body = skill_dst.read_text(encoding="utf-8")
    except OSError:
        body = ""
    if "references/" in body and not (skill_dst.parent / "references").exists():
        print("  warning: skill references/ sidecar is missing. Run 'graphify install' to repair.", file=sys.stderr)
    installed = version_file.read_text(encoding="utf-8").strip()
    if installed != __version__:
        print(f"  warning: skill is from graphify {installed}, package is {__version__}. Run 'graphify install' to update.", file=sys.stderr)


def _refresh_all_version_stamps() -> None:
    """After a successful install, update .graphify_version in all other known skill dirs.

    Prevents stale-version warnings from platforms that were installed previously
    but not explicitly re-installed during this upgrade.
    """
    for name in _PLATFORM_CONFIG:
        skill_dst = _platform_skill_destination(name)
        vf = skill_dst.parent / ".graphify_version"
        if skill_dst.exists():
            vf.write_text(__version__, encoding="utf-8")


def _platform_skill_destination(platform_name: str, *, project: bool = False, project_dir: Path | None = None) -> Path:
    """Return the skill destination for a platform and scope."""
    if platform_name == "gemini":
        if project:
            return (project_dir or Path(".")) / ".gemini" / "skills" / "graphify" / "SKILL.md"
        if platform.system() == "Windows":
            return Path.home() / ".agents" / "skills" / "graphify" / "SKILL.md"
        return Path.home() / ".gemini" / "skills" / "graphify" / "SKILL.md"

    if platform_name == "opencode":
        if project:
            return (project_dir or Path(".")) / ".opencode" / "skills" / "graphify" / "SKILL.md"
        return Path.home() / ".config" / "opencode" / "skills" / "graphify" / "SKILL.md"

    if platform_name == "devin":
        if project:
            return (project_dir or Path(".")) / ".devin" / "skills" / "graphify" / "SKILL.md"
        return Path.home() / ".config" / "devin" / "skills" / "graphify" / "SKILL.md"

    if platform_name == "amp":
        if project:
            return (project_dir or Path(".")) / ".agents" / "skills" / "graphify" / "SKILL.md"
        return Path.home() / ".config" / "agents" / "skills" / "graphify" / "SKILL.md"

    if platform_name in ("antigravity", "antigravity-windows"):
        if project:
            return (project_dir or Path(".")) / ".agents" / "skills" / "graphify" / "SKILL.md"
        # Global Antigravity skill dir (all workspaces): ~/.gemini/config/skills/
        return Path.home() / ".gemini" / "config" / "skills" / "graphify" / "SKILL.md"

    cfg = _PLATFORM_CONFIG[platform_name]
    if project:
        return (project_dir or Path(".")) / cfg["skill_dst"]

    if platform_name in ("claude", "windows") and os.environ.get("CLAUDE_CONFIG_DIR"):
        return Path(os.environ["CLAUDE_CONFIG_DIR"]) / "skills" / "graphify" / "SKILL.md"
    return Path.home() / cfg["skill_dst"]


def _packaged_skill_refs_dir(platform_name: str) -> Path | None:
    """Return the packaged references source dir for a progressive platform, else None.

    A platform opts into progressive disclosure by setting ``skill_refs`` in its
    ``_PLATFORM_CONFIG`` entry. The value names a bundle under
    ``graphify/skills/<bundle>/references/``. Reuse keys (e.g. trae-cn) point at
    their twin's bundle.

    ``gemini`` has no ``_PLATFORM_CONFIG`` entry: it installs claude's
    ``skill.md`` body verbatim (see ``_copy_skill_file``). Since that body is the
    lean progressive core that links to ``references/``, gemini needs claude's
    references/ sidecar too, or its SKILL.md ships with dead pointers. So gemini
    resolves to the claude bundle rather than opting out.

    Bundles ship one platform-group at a time. A host whose bundle directory
    ``graphify/skills/<bundle>/`` is not in this build has not gone progressive
    yet, so this returns None and the host installs today's monolithic SKILL.md
    with no references/ sidecar. Only when the bundle directory IS present does
    this return the references path; if that directory then lacks its
    ``references/`` subdir, ``_copy_skill_file`` hard-fails (a malformed bundle,
    the empty-sidecar regression the wheel-content test also guards).
    """
    if platform_name == "gemini":
        bundle = "claude"
    else:
        bundle = _PLATFORM_CONFIG[platform_name].get("skill_refs")
    if not bundle:
        return None
    bundle_dir = Path(__file__).parent / "skills" / bundle
    if not bundle_dir.is_dir():
        return None
    return bundle_dir / "references"


def _install_skill_references(skill_dst: Path, refs_src: Path) -> None:
    """Atomically install a packaged references/ sidecar next to SKILL.md.

    Stages the packaged dir into ``references.tmp`` (copytree), drops any stale
    ``references/`` already on disk, then ``os.replace``-renames the staged dir
    into place. The rename is atomic on the same filesystem, so an interrupted
    install never leaves a half-written references/ visible to the agent.
    """
    refs_dst = skill_dst.parent / "references"
    refs_staged = skill_dst.parent / "references.tmp"
    if refs_staged.exists():
        shutil.rmtree(refs_staged)
    try:
        shutil.copytree(refs_src, refs_staged)
        if refs_dst.exists():
            shutil.rmtree(refs_dst)
        os.replace(refs_staged, refs_dst)
    except Exception:
        if refs_staged.exists():
            shutil.rmtree(refs_staged, ignore_errors=True)
        raise


def _copy_skill_file(platform_name: str, *, project: bool = False, project_dir: Path | None = None) -> Path:
    """Copy a packaged skill file and write its version stamp.

    For progressive platforms (those with ``skill_refs`` set), the packaged
    ``references/`` sidecar is installed alongside SKILL.md and the single
    ``.graphify_version`` stamp covers both. For monolith platforms (no
    ``skill_refs``), any orphan ``references/`` left by a prior progressive
    install is removed so the on-disk layout matches the package.
    """
    skill_file = "skill.md" if platform_name == "gemini" else _PLATFORM_CONFIG[platform_name]["skill_file"]
    skill_src = Path(__file__).parent / skill_file
    if not skill_src.exists():
        print(f"error: {skill_file} not found in package - reinstall graphify", file=sys.stderr)
        sys.exit(1)

    refs_src = _packaged_skill_refs_dir(platform_name)
    if refs_src is not None and not refs_src.exists():
        # Progressive platform declared a references bundle that is missing from
        # the package. Fail loud rather than silently shipping an empty sidecar.
        print(
            f"error: references for '{platform_name}' not found in package "
            f"({refs_src}) - reinstall graphify",
            file=sys.stderr,
        )
        sys.exit(1)

    skill_dst = _platform_skill_destination(platform_name, project=project, project_dir=project_dir)
    skill_dst.parent.mkdir(parents=True, exist_ok=True)

    # Install the references/ sidecar (or clear an orphan one) BEFORE writing
    # SKILL.md, so SKILL.md is the last artifact laid down. An install that is
    # interrupted partway then leaves no SKILL.md rather than a SKILL.md that
    # points at an absent references/ dir.
    if refs_src is not None:
        _install_skill_references(skill_dst, refs_src)
        print(f"  references       ->  {skill_dst.parent / 'references'}")
    else:
        # Monolith (or progressive-with-no-refs): clear any orphan references/.
        orphan_refs = skill_dst.parent / "references"
        if orphan_refs.exists():
            shutil.rmtree(orphan_refs)

    # SKILL.md last (crash-safety), via an atomic temp + rename.
    tmp_dst = skill_dst.with_suffix(skill_dst.suffix + ".tmp")
    try:
        shutil.copy(skill_src, tmp_dst)
        os.replace(tmp_dst, skill_dst)
    except Exception:
        try:
            tmp_dst.unlink(missing_ok=True)
        except OSError:
            pass
        raise

    (skill_dst.parent / ".graphify_version").write_text(__version__, encoding="utf-8")
    print(f"  skill installed  ->  {skill_dst}")
    return skill_dst


def _remove_skill_file(platform_name: str, *, project: bool = False, project_dir: Path | None = None) -> bool:
    """Remove a platform skill file and its version stamp without touching other scopes."""
    skill_dst = _platform_skill_destination(platform_name, project=project, project_dir=project_dir)
    removed = False
    if skill_dst.exists():
        skill_dst.unlink()
        print(f"  skill removed    ->  {skill_dst}")
        removed = True
    version_file = skill_dst.parent / ".graphify_version"
    if version_file.exists():
        version_file.unlink()
        removed = True
    refs_dir = skill_dst.parent / "references"
    if refs_dir.exists():
        shutil.rmtree(refs_dir)
        removed = True
    for d in (skill_dst.parent, skill_dst.parent.parent, skill_dst.parent.parent.parent):
        try:
            d.rmdir()
        except OSError:
            break
    return removed


def _project_scope_root(path: Path, project_dir: Path) -> Path:
    """Return the top-level project artifact for a project-scoped skill path."""
    try:
        rel = path.relative_to(project_dir)
    except ValueError:
        return path
    return project_dir / rel.parts[0] if rel.parts else path


def _remove_claude_skill_registration(project_dir: Path) -> None:
    """Remove the project-scoped Claude skill registration file/section."""
    claude_md = project_dir / ".claude" / "CLAUDE.md"
    if not claude_md.exists():
        return
    content = claude_md.read_text(encoding="utf-8")
    if "# graphify" not in content:
        return
    cleaned = re.sub(r"\n*# graphify\n.*?(?=\n# |\Z)", "", content, flags=re.DOTALL).rstrip()
    if cleaned:
        claude_md.write_text(cleaned + "\n", encoding="utf-8")
        print(f"  CLAUDE.md        ->  graphify skill registration removed from {claude_md}")
    else:
        claude_md.unlink()
        print(f"  CLAUDE.md        ->  deleted {claude_md}")


def _print_project_git_add_hint(paths: list[Path]) -> None:
    unique: list[str] = []
    for path in paths:
        text = path.as_posix().rstrip("/")
        if path.exists() and path.is_dir():
            text += "/"
        if text not in unique:
            unique.append(text)
    if not unique:
        return
    print()
    print("Project-scoped install. Add to version control:")
    print(f"  git add {' '.join(unique)}")

_SETTINGS_HOOK = {
    # Claude Code v2.1.117+ removed dedicated Grep/Glob tools; searches now go through Bash.
    # We match on Bash and inspect the command string to avoid firing on every shell call.
    "matcher": "Bash",
    "hooks": [
        {
            "type": "command",
            "command": (
                "CMD=$(python3 -c \""
                "import json,sys; d=json.load(sys.stdin); "
                "print(d.get('tool_input',d).get('command',''))\" 2>/dev/null || true); "
                "case \"$CMD\" in "
                r"*grep*|*rg\ *|*ripgrep*|*find\ *|*fd\ *|*ack\ *|*ag\ *) "
                "  [ -f graphify-out/graph.json ] && "
                r"""  echo '{"hookSpecificOutput":{"hookEventName":"PreToolUse","additionalContext":"graphify: knowledge graph at graphify-out/. For focused questions, run `graphify query \"<question>\"` (scoped subgraph, usually much smaller than GRAPH_REPORT.md) instead of grepping raw files. Read GRAPH_REPORT.md only for broad architecture context."}}' """
                "  || true ;; "
                "esac"
            ),
        }
    ],
}

_READ_SETTINGS_HOOK = {
    # The Bash hook above never sees a file read through the native Read tool or a
    # Glob, which is the most common way an agent skips the graph: answering a
    # codebase question by Read-ing many source files one by one (issue #1114).
    # Match Read|Glob, inspect the target path, and nudge (never block) only for a
    # source/doc file outside graphify-out/ when a graph exists. The parser is
    # python3 (already a graphify dependency), the shell is POSIX, and every branch
    # fails open, so a legitimate read always goes through. Reading the graph's own
    # report under graphify-out/ is suppressed so it never starts a feedback loop.
    "matcher": "Read|Glob",
    "hooks": [
        {
            "type": "command",
            "command": (
                "HIT=$(python3 -c \""
                "import json,sys;"
                "d=json.load(sys.stdin);"
                "t=d.get('tool_input',d);"
                "s=(str(t.get('file_path') or '')+' '+str(t.get('pattern') or '')+' '+str(t.get('path') or '')).lower().replace(chr(92),'/');"
                "exts=('.py','.js','.ts','.tsx','.jsx','.go','.rs','.java','.rb','.c','.h','.cpp','.hpp','.cc','.cs','.kt','.swift','.php','.scala','.lua','.sh','.md','.rst','.txt','.mdx');"
                "sys.stdout.write('1' if 'graphify-out/' not in s and any(e in s for e in exts) else '')\" 2>/dev/null || true); "
                "if [ \"$HIT\" = 1 ] && [ -f graphify-out/graph.json ]; then "
                r"""echo '{"hookSpecificOutput":{"hookEventName":"PreToolUse","additionalContext":"graphify: knowledge graph at graphify-out/. For codebase questions, run `graphify query \"<question>\"` (scoped subgraph, usually much smaller than reading files one by one), `graphify explain \"<concept>\"`, or `graphify path \"<A>\" \"<B>\"`, instead of reading source files to answer. Read raw files to modify or debug specific code, or when the graph lacks the detail."}}'; """
                "fi || true"
            ),
        }
    ],
}

def _skill_registration(skill_path: str = "~/.claude/skills/graphify/SKILL.md") -> str:
    return (
        "\n# graphify\n"
        f"- **graphify** (`{skill_path}`) "
        "- any input to knowledge graph. Trigger: `/graphify`\n"
        "When the user types `/graphify`, invoke the Skill tool "
        "with `skill: \"graphify\"` before doing anything else.\n"
    )


_PLATFORM_CONFIG: dict[str, dict] = {
    "claude": {
        "skill_file": "skill.md",
        "skill_dst": Path(".claude") / "skills" / "graphify" / "SKILL.md",
        "claude_md": True,
        "skill_refs": "claude",
    },
    "codex": {
        "skill_file": "skill-codex.md",
        "skill_dst": Path(".codex") / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
        "skill_refs": "codex",
    },
    "opencode": {
        "skill_file": "skill-opencode.md",
        "skill_dst": Path(".config") / "opencode" / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
        "skill_refs": "opencode",
    },
    "kilo": {
        "skill_file": "skill-kilo.md",
        "skill_dst": Path(".config") / "kilo" / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
        "skill_refs": "kilo",
    },
    "aider": {
        # Monolith: aider ships the full SKILL.md inline, no references/ sidecar.
        "skill_file": "skill-aider.md",
        "skill_dst": Path(".aider") / "graphify" / "SKILL.md",
        "claude_md": False,
    },
    "copilot": {
        "skill_file": "skill-copilot.md",
        "skill_dst": Path(".copilot") / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
        "skill_refs": "copilot",
    },
    "claw": {
        "skill_file": "skill-claw.md",
        "skill_dst": Path(".openclaw") / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
        "skill_refs": "claw",
    },
    "droid": {
        "skill_file": "skill-droid.md",
        "skill_dst": Path(".factory") / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
        "skill_refs": "droid",
    },
    "trae": {
        "skill_file": "skill-trae.md",
        "skill_dst": Path(".trae") / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
        "skill_refs": "trae",
    },
    "trae-cn": {
        # Reuses trae's split bundle (same skill body + references).
        "skill_file": "skill-trae.md",
        "skill_dst": Path(".trae-cn") / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
        "skill_refs": "trae",
    },
    "hermes": {
        # Reuses claw's split bundle.
        "skill_file": "skill-claw.md",
        "skill_dst": Path(".hermes") / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
        "skill_refs": "claw",
    },
    "kiro": {
        "skill_file": "skill-kiro.md",
        "skill_dst": Path(".kiro") / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
        "skill_refs": "kiro",
    },
    "pi": {
        "skill_file": "skill-pi.md",
        "skill_dst": Path(".pi") / "agent" / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
        "skill_refs": "pi",
    },
    "codebuddy": {
        # Reuses claude's split bundle (shares skill.md).
        "skill_file": "skill.md",
        "skill_dst": Path(".codebuddy") / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
        "skill_refs": "claude",
    },
    "antigravity": {
        # Rides claude's split bundle (shares skill.md).
        "skill_file": "skill.md",
        "skill_dst": Path(".agents") / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
        "skill_refs": "claude",
    },
    "antigravity-windows": {
        # Rides windows' split bundle.
        "skill_file": "skill-windows.md",
        "skill_dst": Path(".agents") / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
        "skill_refs": "windows",
    },
    "windows": {
        "skill_file": "skill-windows.md",
        "skill_dst": Path(".claude") / "skills" / "graphify" / "SKILL.md",
        "claude_md": True,
        "skill_refs": "windows",
    },
    "kimi": {
        # Reuses claude's split bundle (shares skill.md).
        "skill_file": "skill.md",
        "skill_dst": Path(".kimi") / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
        "skill_refs": "claude",
    },
    "amp": {
        # Amp searches .agents/skills (project) and ~/.config/agents/skills (user),
        # not .amp/skills. The user-scope path is set in _platform_skill_destination.
        "skill_file": "skill-amp.md",
        "skill_dst": Path(".agents") / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
        "skill_refs": "amp",
    },
    "devin": {
        # Monolith: devin ships the full SKILL.md inline, no references/ sidecar.
        "skill_file": "skill-devin.md",
        # User scope: ~/.config/devin/skills/graphify/SKILL.md
        # Project scope: .devin/skills/graphify/SKILL.md (overridden in _platform_skill_destination)
        "skill_dst": Path(".config") / "devin" / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
    },
}


def _replace_or_append_section(content: str, marker: str, new_section: str) -> str:
    """Idempotently update or append a graphify-owned section in shared files.

    If ``marker`` is not in ``content``, append ``new_section`` to the end
    (with a blank-line separator if there's existing content).

    If ``marker`` IS in ``content``, replace the existing section in place.
    The section runs from the first line containing ``marker`` to the line
    before the next H2 heading (``## `` at line start), or to EOF if no later
    H2 exists. This lets older installs receive the updated copy without
    users having to uninstall and reinstall — important for the issue #580
    fix where existing report-first text would otherwise silently linger.
    """
    if marker not in content:
        if content.strip():
            return content.rstrip() + "\n\n" + new_section.lstrip()
        return new_section.lstrip()

    lines = content.split("\n")
    start = next((i for i, line in enumerate(lines) if marker in line), None)
    if start is None:
        return content.rstrip() + "\n\n" + new_section.lstrip()

    end = len(lines)
    for j in range(start + 1, len(lines)):
        if lines[j].startswith("## "):
            end = j
            break

    head = "\n".join(lines[:start]).rstrip()
    tail = "\n".join(lines[end:]).lstrip()
    section = new_section.strip()

    parts: list[str] = []
    if head:
        parts.append(head)
    parts.append(section)
    if tail:
        parts.append(tail)
    out = "\n\n".join(parts)
    if not out.endswith("\n"):
        out += "\n"
    return out


def _print_banner() -> None:
    """Amber brain banner on graphify install. TTY-only, never raises."""
    if not sys.stdout.isatty():
        return
    try:
        if sys.platform == "win32":
            import ctypes
            ctypes.windll.kernel32.SetConsoleMode(
                ctypes.windll.kernel32.GetStdHandle(-11), 7
            )
        A = "\033[38;5;214m"
        D = "\033[38;5;130m"
        R = "\033[0m"
        print(f"""{A}
  ╭──◉──╮     ╭──◉──╮
 ╱  ◉   ◉ ╲ ╱ ◉   ◉  ╲
│   ◉─◉─◉  ◉  ◉─◉─◉   │
│    ◉   ◉ │ ◉   ◉    │
│   ◉─◉─◉  ◉  ◉─◉─◉   │
 ╲  ◉   ◉ ╱ ╲ ◉   ◉  ╱
  ╰──◉──╯     ╰──◉──╯
           ◉

  █▀▀ █▀█ ▄▀█ █▀█ █ █ █ █▀▀ █▄█
  █▄█ █▀▄ █▀█ █▀▀ █▀█ █ █▀   █{D}  {__version__}{R}
""")
    except Exception:
        pass


def install(platform: str = "claude", *, project: bool = False, project_dir: Path | None = None) -> None:
    _print_banner()
    if platform == "gemini":
        gemini_install(project_dir=project_dir, project=project)
        return
    if platform == "cursor":
        _cursor_install(Path("."))
        return
    # On Windows, antigravity needs the PowerShell skill, not the bash one
    if platform == "antigravity" and sys.platform == "win32":
        platform = "antigravity-windows"
    if platform not in _PLATFORM_CONFIG:
        print(
            f"error: unknown platform '{platform}'. Choose from: {', '.join(_PLATFORM_CONFIG)}, gemini, cursor",
            file=sys.stderr,
        )
        sys.exit(1)

    cfg = _PLATFORM_CONFIG[platform]
    project_dir = project_dir or Path(".")
    skill_dst = _copy_skill_file(platform, project=project, project_dir=project_dir)

    if platform == "kilo":
        # Kilo Code also supports a native /graphify command file.
        command_src = Path(__file__).parent / "command-kilo.md"
        if not command_src.exists():
            print(
                f"error: command-kilo.md not found in package - reinstall graphify",
                file=sys.stderr,
            )
            sys.exit(1)
        command_dst = Path.home() / ".config" / "kilo" / "command" / "graphify.md"
        command_dst.parent.mkdir(parents=True, exist_ok=True)
        shutil.copy(command_src, command_dst)
        print(f"  command installed ->  {command_dst}")

    if cfg["claude_md"]:
        # Register in the matching Claude Code scope.
        claude_md = (project_dir / ".claude" / "CLAUDE.md") if project else Path.home() / ".claude" / "CLAUDE.md"
        registration = _skill_registration(".claude/skills/graphify/SKILL.md" if project else "~/.claude/skills/graphify/SKILL.md")
        if claude_md.exists():
            content = claude_md.read_text(encoding="utf-8")
            if "graphify" in content:
                print(f"  CLAUDE.md        ->  already registered (no change)")
            else:
                claude_md.write_text(content.rstrip() + registration, encoding="utf-8")
                print(f"  CLAUDE.md        ->  skill registered in {claude_md}")
        else:
            claude_md.parent.mkdir(parents=True, exist_ok=True)
            claude_md.write_text(registration.lstrip(), encoding="utf-8")
            print(f"  CLAUDE.md        ->  created at {claude_md}")

    if platform == "codebuddy":
        # Register in ~/.codebuddy/CODEBUDDY.md (CodeBuddy only)
        codebuddy_md = Path.home() / ".codebuddy" / "CODEBUDDY.md"
        registration = _skill_registration("~/.codebuddy/skills/graphify/SKILL.md")
        if codebuddy_md.exists():
            content = codebuddy_md.read_text(encoding="utf-8")
            if "graphify" in content:
                print(f"  CODEBUDDY.md     ->  already registered (no change)")
            else:
                codebuddy_md.write_text(content.rstrip() + registration, encoding="utf-8")
                print(f"  CODEBUDDY.md     ->  skill registered in {codebuddy_md}")
        else:
            codebuddy_md.parent.mkdir(parents=True, exist_ok=True)
            codebuddy_md.write_text(registration.lstrip(), encoding="utf-8")
            print(f"  CODEBUDDY.md     ->  created at {codebuddy_md}")

    if platform == "opencode":
        _install_opencode_plugin(project_dir if project else Path("."))

    # Refresh version stamps in all other previously-installed skill dirs so
    # stale-version warnings don't fire for platforms not explicitly re-installed.
    if project:
        _print_project_git_add_hint([_project_scope_root(skill_dst, project_dir)])
    else:
        _refresh_all_version_stamps()

    print()
    print("Done. Open your AI coding assistant and type:")
    print()
    print("  /graphify .")
    print()


def _print_install_usage() -> None:
    platforms = ", ".join([*_PLATFORM_CONFIG, "gemini", "cursor"])
    print("Usage: graphify install [--project] [--platform P|P]")
    print(f"Platforms: {platforms}")


# The always-on instruction blocks are packaged markdown under graphify/always_on/,
# generated by tools/skillgen and guarded by `skillgen --check`. Reading them at
# load keeps the install-string / issue-#580 contract byte-for-byte while letting
# a human edit one fragment instead of a triple-quoted literal here.

_CLAUDE_MD_MARKER = "## graphify"

_CODEBUDDY_MD_MARKER = "## graphify"

# AGENTS.md section for Codex, OpenCode, and OpenClaw.
# All three platforms read AGENTS.md in the project root for persistent instructions.

_AGENTS_MD_MARKER = "## graphify"


_GEMINI_MD_MARKER = "## graphify"

_GEMINI_HOOK = {
    "matcher": "read_file|list_directory",
    "hooks": [
        {
            "type": "command",
            "command": (
                'python -c "'
                "import sys,pathlib,json;"
                "e=pathlib.Path('graphify-out/graph.json').exists();"
                "d={'decision':'allow'};"
                "e and d.update({'additionalContext':'graphify: knowledge graph at graphify-out/. For focused questions, run `graphify query \"<question>\"` (scoped subgraph, usually much smaller than GRAPH_REPORT.md) instead of grepping raw files. Read GRAPH_REPORT.md only for broad architecture context.'});"
                "sys.stdout.write(json.dumps(d))"
                '"'
            ),
        }
    ],
}


def gemini_install(project_dir: Path | None = None, *, project: bool = False) -> None:
    """Copy skill file, write GEMINI.md section, and install BeforeTool hook."""
    project_dir = project_dir or Path(".")
    skill_dst = _copy_skill_file("gemini", project=project, project_dir=project_dir)

    target = project_dir / "GEMINI.md"

    if target.exists():
        content = target.read_text(encoding="utf-8")
        new_content = _replace_or_append_section(
            content, _GEMINI_MD_MARKER, _always_on("gemini-md")
        )
    else:
        new_content = _always_on("gemini-md")

    if target.exists() and new_content == target.read_text(encoding="utf-8"):
        print(f"graphify already configured in {target.resolve()} (no change)")
    else:
        target.write_text(new_content, encoding="utf-8")
        print(f"graphify section written to {target.resolve()}")

    # Always re-install the Gemini hook so an older payload (e.g. pre-issue-#580
    # wording) is replaced on upgrade.
    _install_gemini_hook(project_dir)
    if project:
        _print_project_git_add_hint([_project_scope_root(skill_dst, project_dir), project_dir / "GEMINI.md", project_dir / ".gemini"])
    print()
    print("Gemini CLI will now check the knowledge graph before answering")
    print("codebase questions and rebuild it after code changes.")


def _install_gemini_hook(project_dir: Path) -> None:
    settings_path = project_dir / ".gemini" / "settings.json"
    settings_path.parent.mkdir(parents=True, exist_ok=True)
    try:
        settings = (
            json.loads(settings_path.read_text(encoding="utf-8"))
            if settings_path.exists()
            else {}
        )
    except json.JSONDecodeError:
        settings = {}
    before_tool = settings.setdefault("hooks", {}).setdefault("BeforeTool", [])
    settings["hooks"]["BeforeTool"] = [
        h for h in before_tool if "graphify" not in str(h)
    ]
    settings["hooks"]["BeforeTool"].append(_GEMINI_HOOK)
    settings_path.write_text(json.dumps(settings, indent=2), encoding="utf-8")
    print("  .gemini/settings.json  ->  BeforeTool hook registered")


def _uninstall_gemini_hook(project_dir: Path) -> None:
    settings_path = project_dir / ".gemini" / "settings.json"
    if not settings_path.exists():
        return
    try:
        settings = json.loads(settings_path.read_text(encoding="utf-8"))
    except json.JSONDecodeError:
        return
    before_tool = settings.get("hooks", {}).get("BeforeTool", [])
    filtered = [h for h in before_tool if "graphify" not in str(h)]
    if len(filtered) == len(before_tool):
        return
    settings["hooks"]["BeforeTool"] = filtered
    settings_path.write_text(json.dumps(settings, indent=2), encoding="utf-8")
    print("  .gemini/settings.json  ->  BeforeTool hook removed")


def gemini_uninstall(project_dir: Path | None = None, *, project: bool = False) -> None:
    """Remove the graphify section from GEMINI.md, uninstall hook, and remove skill file."""
    project_dir = project_dir or Path(".")
    _remove_skill_file("gemini", project=project, project_dir=project_dir)

    target = project_dir / "GEMINI.md"
    if not target.exists():
        print("No GEMINI.md found in current directory - nothing to do")
        return
    content = target.read_text(encoding="utf-8")
    if _GEMINI_MD_MARKER not in content:
        print("graphify section not found in GEMINI.md - nothing to do")
        return
    cleaned = re.sub(
        r"\n*## graphify\n.*?(?=\n## |\Z)", "", content, flags=re.DOTALL
    ).rstrip()
    if cleaned:
        target.write_text(cleaned + "\n", encoding="utf-8")
        print(f"graphify section removed from {target.resolve()}")
    else:
        target.unlink()
        print(f"GEMINI.md was empty after removal - deleted {target.resolve()}")
    _uninstall_gemini_hook(project_dir)


_VSCODE_INSTRUCTIONS_MARKER = "## graphify"


def vscode_install(project_dir: Path | None = None) -> None:
    """Install graphify skill for VS Code Copilot Chat + write .github/copilot-instructions.md."""
    skill_src = Path(__file__).parent / "skill-vscode.md"
    refs_bundle = "vscode"
    if not skill_src.exists():
        skill_src = Path(__file__).parent / "skill-copilot.md"
        refs_bundle = "copilot"
    skill_dst = Path.home() / ".copilot" / "skills" / "graphify" / "SKILL.md"
    skill_dst.parent.mkdir(parents=True, exist_ok=True)
    tmp_dst = skill_dst.with_suffix(skill_dst.suffix + ".tmp")
    try:
        shutil.copy(skill_src, tmp_dst)
        os.replace(tmp_dst, skill_dst)
    except Exception:
        try:
            tmp_dst.unlink(missing_ok=True)
        except OSError:
            pass
        raise
    # Progressive-capable: install the packaged references/ sidecar when present.
    refs_src = Path(__file__).parent / "skills" / refs_bundle / "references"
    if refs_src.exists():
        _install_skill_references(skill_dst, refs_src)
        print(f"  references       ->  {skill_dst.parent / 'references'}")
    else:
        orphan_refs = skill_dst.parent / "references"
        if orphan_refs.exists():
            shutil.rmtree(orphan_refs)
    (skill_dst.parent / ".graphify_version").write_text(__version__, encoding="utf-8")
    print(f"  skill installed  ->  {skill_dst}")

    instructions = (project_dir or Path(".")) / ".github" / "copilot-instructions.md"
    instructions.parent.mkdir(parents=True, exist_ok=True)
    if instructions.exists():
        content = instructions.read_text(encoding="utf-8")
        new_content = _replace_or_append_section(
            content, _VSCODE_INSTRUCTIONS_MARKER, _always_on("vscode-instructions")
        )
        if new_content == content:
            print(f"  {instructions}  ->  already configured (no change)")
        else:
            instructions.write_text(new_content, encoding="utf-8")
            print(f"  {instructions}  ->  graphify section {'updated' if _VSCODE_INSTRUCTIONS_MARKER in content else 'added'}")
    else:
        instructions.write_text(_always_on("vscode-instructions"), encoding="utf-8")
        print(f"  {instructions}  ->  created")

    print()
    print(
        "VS Code Copilot Chat configured. Type /graphify in the chat panel to build the graph."
    )
    print("Note: for GitHub Copilot CLI (terminal), use: graphify copilot install")


def vscode_uninstall(project_dir: Path | None = None) -> None:
    """Remove graphify VS Code Copilot Chat skill and .github/copilot-instructions.md section."""
    skill_dst = Path.home() / ".copilot" / "skills" / "graphify" / "SKILL.md"
    if skill_dst.exists():
        skill_dst.unlink()
        print(f"  skill removed    ->  {skill_dst}")
    version_file = skill_dst.parent / ".graphify_version"
    if version_file.exists():
        version_file.unlink()
    refs_dir = skill_dst.parent / "references"
    if refs_dir.exists():
        shutil.rmtree(refs_dir)
    for d in (
        skill_dst.parent,
        skill_dst.parent.parent,
        skill_dst.parent.parent.parent,
    ):
        try:
            d.rmdir()
        except OSError:
            break

    instructions = (project_dir or Path(".")) / ".github" / "copilot-instructions.md"
    if not instructions.exists():
        return
    content = instructions.read_text(encoding="utf-8")
    if _VSCODE_INSTRUCTIONS_MARKER not in content:
        return
    cleaned = re.sub(
        r"\n*## graphify\n.*?(?=\n## |\Z)", "", content, flags=re.DOTALL
    ).rstrip()
    if cleaned:
        instructions.write_text(cleaned + "\n", encoding="utf-8")
        print(f"  graphify section removed from {instructions}")
    else:
        instructions.unlink()
        print(f"  {instructions}  ->  deleted (was empty after removal)")


_ANTIGRAVITY_RULES_PATH = Path(".agents") / "rules" / "graphify.md"
_ANTIGRAVITY_WORKFLOW_PATH = Path(".agents") / "workflows" / "graphify.md"


_ANTIGRAVITY_WORKFLOW = """\
---
name: graphify
description: Turn any folder of files into a navigable knowledge graph
---

# Workflow: graphify

Follow the graphify skill installed at ~/.gemini/config/skills/graphify/SKILL.md to run the full pipeline.

If no path argument is given, use `.` (current directory).
"""



_KIRO_STEERING_MARKER = "graphify: A knowledge graph of this project"


def _kiro_install(project_dir: Path) -> None:
    """Write graphify skill + steering file for Kiro IDE/CLI."""
    project_dir = project_dir or Path(".")

    # Skill file + references/ sidecar + .graphify_version stamp via the shared
    # progressive-disclosure helper.  Previously this used a bare write_text that
    # bypassed _copy_skill_file, so the references/ dir and version stamp were
    # never written even though kiro declares skill_refs: "kiro" (#1142).
    _copy_skill_file("kiro", project=True, project_dir=project_dir)

    # Steering file → .kiro/steering/graphify.md (always-on)
    steering_dir = project_dir / ".kiro" / "steering"
    steering_dir.mkdir(parents=True, exist_ok=True)
    steering_dst = steering_dir / "graphify.md"
    if steering_dst.exists() and steering_dst.read_text(encoding="utf-8") == _always_on("kiro-steering"):
        print(f"  .kiro/steering/graphify.md  ->  already configured (no change)")
    else:
        # File is wholly graphify-owned. Overwrite on upgrade so older
        # report-first wording does not silently linger (issue #580).
        action = "updated" if steering_dst.exists() else "written"
        steering_dst.write_text(_always_on("kiro-steering"), encoding="utf-8")
        print(f"  .kiro/steering/graphify.md  ->  always-on steering {action}")

    print()
    print("Kiro will now read the knowledge graph before every conversation.")
    print("Use /graphify to build or update the graph.")


def _kiro_uninstall(project_dir: Path) -> None:
    """Remove graphify skill + steering file for Kiro."""
    project_dir = project_dir or Path(".")
    removed = []

    # Skill + .graphify_version + references/ sidecar + empty-dir walk.
    skill_dst = _platform_skill_destination("kiro", project=True, project_dir=project_dir)
    if _remove_skill_file("kiro", project=True, project_dir=project_dir):
        removed.append(str(skill_dst.relative_to(project_dir)))

    steering_dst = project_dir / ".kiro" / "steering" / "graphify.md"
    if steering_dst.exists():
        steering_dst.unlink()
        removed.append(str(steering_dst.relative_to(project_dir)))

    print("Removed: " + (", ".join(removed) if removed else "nothing to remove"))


def _antigravity_finalize(skill_dst: Path, project_dir: Path) -> None:
    """Write Antigravity's always-on layer next to an installed skill.

    Injects the native tool-discovery YAML frontmatter into *skill_dst*, then
    writes ``.agents/rules/graphify.md`` and ``.agents/workflows/graphify.md``
    under *project_dir*. Shared by the global ``antigravity install`` and the
    project-scoped ``install --project --platform antigravity`` paths, so both lay
    down the rules/workflows that the uninstall path already expects to remove.
    """
    # Inject YAML frontmatter for native Antigravity tool discovery.
    if skill_dst.exists():
        content = skill_dst.read_text(encoding="utf-8")
        if not content.startswith("---\n"):
            frontmatter = "---\nname: graphify-manager\ndescription: Rebuild the code graph or perform manual CLI queries when MCP server is offline.\n---\n\n"
            skill_dst.write_text(frontmatter + content, encoding="utf-8")

    # .agents/rules/graphify.md
    rules_path = project_dir / _ANTIGRAVITY_RULES_PATH
    rules_path.parent.mkdir(parents=True, exist_ok=True)
    if rules_path.exists():
        existing = rules_path.read_text(encoding="utf-8")
        if _always_on("antigravity-rules").strip() != existing.strip():
            rules_path.write_text(_always_on("antigravity-rules"), encoding="utf-8")
            print(f"graphify rule updated at {rules_path.resolve()}")
        else:
            print(f"graphify rule already configured at {rules_path.resolve()} (no change)")
    else:
        rules_path.write_text(_always_on("antigravity-rules"), encoding="utf-8")
        print(f"graphify rule written to {rules_path.resolve()}")

    # .agents/workflows/graphify.md
    wf_path = project_dir / _ANTIGRAVITY_WORKFLOW_PATH
    wf_path.parent.mkdir(parents=True, exist_ok=True)
    if wf_path.exists():
        existing = wf_path.read_text(encoding="utf-8")
        if _ANTIGRAVITY_WORKFLOW.strip() != existing.strip():
            wf_path.write_text(_ANTIGRAVITY_WORKFLOW, encoding="utf-8")
            print(f"graphify workflow updated at {wf_path.resolve()}")
        else:
            print(f"graphify workflow already configured at {wf_path.resolve()} (no change)")
    else:
        wf_path.write_text(_ANTIGRAVITY_WORKFLOW, encoding="utf-8")
        print(f"graphify workflow written to {wf_path.resolve()}")


def _antigravity_install(project_dir: Path) -> None:
    """Install graphify for Google Antigravity (global skill + .agents/rules + .agents/workflows)."""
    # Copy the skill to ~/.gemini/config/skills/graphify/SKILL.md (global), then
    # lay down the always-on rules/workflows under the project dir.
    install(platform="antigravity")
    _antigravity_finalize(_platform_skill_destination("antigravity"), project_dir)

    print()
    print("Antigravity will now check the knowledge graph before answering")
    print("codebase questions. Run /graphify first to build the graph.")
    print()
    print(
        "To enable full MCP architecture navigation, add this to ~/.gemini/antigravity/mcp_config.json:"
    )
    print('  "graphify": {')
    print('    "command": "uv",')
    print(
        '    "args": ["run", "--with", "graphifyy", "--with", "mcp", "-m", "graphify.serve", "${workspace.path}/graphify-out/graph.json"]'
    )
    print("  }")


def _antigravity_uninstall(project_dir: Path, *, project: bool = False) -> None:
    """Remove graphify Antigravity rules, workflow, and skill files."""
    # Remove rules file
    rules_path = project_dir / _ANTIGRAVITY_RULES_PATH
    if rules_path.exists():
        rules_path.unlink()
        print(f"graphify rule removed from {rules_path.resolve()}")
    else:
        print("No graphify Antigravity rule found - nothing to do")

    # Remove workflow file
    wf_path = project_dir / _ANTIGRAVITY_WORKFLOW_PATH
    if wf_path.exists():
        wf_path.unlink()
        print(f"graphify workflow removed from {wf_path.resolve()}")

    # Remove skill file
    skill_dst = _platform_skill_destination("antigravity", project=project, project_dir=project_dir)
    if skill_dst.exists():
        skill_dst.unlink()
        print(f"graphify skill removed from {skill_dst}")
    version_file = skill_dst.parent / ".graphify_version"
    if version_file.exists():
        version_file.unlink()
    refs_dir = skill_dst.parent / "references"
    if refs_dir.exists():
        shutil.rmtree(refs_dir)
    for d in (
        skill_dst.parent,
        skill_dst.parent.parent,
        skill_dst.parent.parent.parent,
    ):
        try:
            d.rmdir()
        except OSError:
            break


_CURSOR_RULE_PATH = Path(".cursor") / "rules" / "graphify.mdc"
_CURSOR_RULE = """\
---
description: graphify knowledge graph context
alwaysApply: true
---

This project has a graphify knowledge graph at graphify-out/.

- For codebase or architecture questions, when `graphify-out/graph.json` exists, first run `graphify query "<question>"` (or `graphify path "<A>" "<B>"` / `graphify explain "<concept>"`). These return a scoped subgraph, usually much smaller than `GRAPH_REPORT.md` or raw grep output.
- If graphify-out/wiki/index.md exists, navigate it instead of reading raw files
- Read graphify-out/GRAPH_REPORT.md only for broad architecture review or when query/path/explain do not surface enough context
- After modifying code files in this session, run `graphify update .` to keep the graph current (AST-only, no API cost)
"""


def _cursor_install(project_dir: Path) -> None:
    """Write .cursor/rules/graphify.mdc with alwaysApply: true."""
    rule_path = (project_dir or Path(".")) / _CURSOR_RULE_PATH
    rule_path.parent.mkdir(parents=True, exist_ok=True)
    if rule_path.exists() and rule_path.read_text(encoding="utf-8") == _CURSOR_RULE:
        print(f"graphify rule at {rule_path} already configured (no change)")
        return
    # File is wholly graphify-owned. Overwrite on upgrade so older
    # report-first wording does not silently linger (issue #580).
    action = "updated" if rule_path.exists() else "written"
    rule_path.write_text(_CURSOR_RULE, encoding="utf-8")
    print(f"graphify rule {action} at {rule_path.resolve()}")
    print()
    print("Cursor will now always include the knowledge graph context.")
    print("Run /graphify . first to build the graph if you haven't already.")


def _cursor_uninstall(project_dir: Path) -> None:
    """Remove .cursor/rules/graphify.mdc."""
    rule_path = (project_dir or Path(".")) / _CURSOR_RULE_PATH
    if not rule_path.exists():
        print("No graphify Cursor rule found - nothing to do")
        return
    rule_path.unlink()
    print(f"graphify Cursor rule removed from {rule_path.resolve()}")


# Devin CLI — .windsurf/rules/graphify.md (always-on context)
# Devin reads .windsurf/rules/*.md files the same way Windsurf IDE does.
_DEVIN_RULES_PATH = Path(".windsurf") / "rules" / "graphify.md"
_DEVIN_RULES = """\
## graphify

This project has a graphify knowledge graph at graphify-out/.

Rules:
- For codebase or architecture questions, when `graphify-out/graph.json` exists, first run `graphify query "<question>"` (or `graphify path "<A>" "<B>"` / `graphify explain "<concept>"`). These return a scoped subgraph, usually much smaller than `GRAPH_REPORT.md` or raw grep output.
- If graphify-out/wiki/index.md exists, navigate it instead of reading raw files
- Read graphify-out/GRAPH_REPORT.md only for broad architecture review or when query/path/explain do not surface enough context
- After modifying code files in this session, run `graphify update .` to keep the graph current (AST-only, no API cost)
"""


def _devin_rules_install(project_dir: Path) -> None:
    """Write .windsurf/rules/graphify.md for always-on Devin context."""
    rules_path = (project_dir or Path(".")) / _DEVIN_RULES_PATH
    rules_path.parent.mkdir(parents=True, exist_ok=True)
    if rules_path.exists() and rules_path.read_text(encoding="utf-8") == _DEVIN_RULES:
        print(f"  {rules_path}  ->  already configured (no change)")
        return
    action = "updated" if rules_path.exists() else "written"
    rules_path.write_text(_DEVIN_RULES, encoding="utf-8")
    print(f"  rules {action}  ->  {rules_path}")


def _devin_rules_uninstall(project_dir: Path) -> None:
    """Remove .windsurf/rules/graphify.md."""
    rules_path = (project_dir or Path(".")) / _DEVIN_RULES_PATH
    if not rules_path.exists():
        return
    rules_path.unlink()
    print(f"  rules removed  ->  {rules_path}")


_KILO_PLUGIN_JS = """\
// graphify Kilo plugin
// Injects a knowledge graph reminder before bash tool calls when the graph exists.
import { existsSync } from "fs";
import { join } from "path";

export const GraphifyPlugin = async ({ directory }) => {
  let reminded = false;

  return {
    "tool.execute.before": async (input, output) => {
      if (reminded) return;
      if (!existsSync(join(directory, "graphify-out", "graph.json"))) return;

      if (input.tool === "bash") {
        output.args.command =
          'echo "[graphify] Knowledge graph available. Read graphify-out/GRAPH_REPORT.md for god nodes and architecture context before searching files." && ' +
          output.args.command;
        reminded = true;
      }
    },
  };
};
"""

_KILO_PLUGIN_PATH = Path(".kilo") / "plugins" / "graphify.js"
_KILO_CONFIG_JSON_PATH = Path(".kilo") / "kilo.json"
_KILO_CONFIG_JSONC_PATH = Path(".kilo") / "kilo.jsonc"


def _strip_json_comments(raw: str) -> str:
    """Remove JSONC-style comments while leaving string content intact."""
    result: list[str] = []
    in_string = False
    escaped = False
    line_comment = False
    block_comment = False
    i = 0

    while i < len(raw):
        ch = raw[i]
        nxt = raw[i + 1] if i + 1 < len(raw) else ""

        if line_comment:
            if ch == "\n":
                line_comment = False
                result.append(ch)
            i += 1
            continue

        if block_comment:
            if ch == "*" and nxt == "/":
                block_comment = False
                i += 2
            else:
                i += 1
            continue

        if in_string:
            result.append(ch)
            if escaped:
                escaped = False
            elif ch == "\\":
                escaped = True
            elif ch == '"':
                in_string = False
            i += 1
            continue

        if ch == "/" and nxt == "/":
            line_comment = True
            i += 2
            continue
        if ch == "/" and nxt == "*":
            block_comment = True
            i += 2
            continue

        result.append(ch)
        if ch == '"':
            in_string = True
        i += 1

    return re.sub(r",(\s*[}\]])", r"\1", "".join(result))


def _load_json_like(config_file: Path) -> dict:
    if not config_file.exists():
        return {}
    try:
        raw = config_file.read_text(encoding="utf-8")
        if config_file.suffix == ".jsonc":
            raw = _strip_json_comments(raw)
        loaded = json.loads(raw)
    except (OSError, json.JSONDecodeError):
        return {}
    return loaded if isinstance(loaded, dict) else {}


def _kilo_config_path(project_dir: Path) -> Path:
    kilo_dir = (project_dir or Path(".")) / ".kilo"
    json_path = kilo_dir / _KILO_CONFIG_JSON_PATH.name
    if json_path.exists():
        return json_path
    jsonc_path = kilo_dir / _KILO_CONFIG_JSONC_PATH.name
    if jsonc_path.exists():
        return jsonc_path
    return json_path


def _kilo_config_write_path(project_dir: Path) -> Path:
    """Write automated Kilo edits to kilo.json so existing JSONC stays untouched."""
    kilo_dir = (project_dir or Path(".")) / ".kilo"
    return kilo_dir / _KILO_CONFIG_JSON_PATH.name


def _install_kilo_plugin(project_dir: Path) -> None:
    """Write graphify.js plugin and register it without rewriting user JSONC."""
    plugin_file = project_dir / _KILO_PLUGIN_PATH
    plugin_file.parent.mkdir(parents=True, exist_ok=True)
    plugin_file.write_text(_KILO_PLUGIN_JS, encoding="utf-8")
    print(f"  {_KILO_PLUGIN_PATH}  ->  tool.execute.before hook written")

    config_file = _kilo_config_path(project_dir)
    write_config_file = _kilo_config_write_path(project_dir)
    write_config_file.parent.mkdir(parents=True, exist_ok=True)
    config = _load_json_like(config_file)
    plugins = config.get("plugin")
    if not isinstance(plugins, list):
        plugins = []
        config["plugin"] = plugins
    entry = plugin_file.resolve().as_uri()
    if entry not in plugins:
        plugins.append(entry)
        write_config_file.write_text(json.dumps(config, indent=2), encoding="utf-8")
        print(f"  {write_config_file.relative_to(project_dir)}  ->  plugin registered")
    else:
        print(
            f"  {config_file.relative_to(project_dir)}  ->  plugin already registered (no change)"
        )


def _uninstall_kilo_plugin(project_dir: Path) -> None:
    """Remove graphify.js plugin and deregister it without rewriting user JSONC."""
    plugin_file = project_dir / _KILO_PLUGIN_PATH
    if plugin_file.exists():
        plugin_file.unlink()
        print(f"  {_KILO_PLUGIN_PATH}  ->  removed")

    config_file = _kilo_config_path(project_dir)
    if not config_file.exists():
        return
    write_config_file = _kilo_config_write_path(project_dir)
    config = _load_json_like(config_file)
    plugins = config.get("plugin", [])
    if not isinstance(plugins, list):
        plugins = []
    entry = plugin_file.resolve().as_uri()
    if entry in plugins:
        config["plugin"] = [plugin for plugin in plugins if plugin != entry]
        if not config["plugin"]:
            config.pop("plugin")
        write_config_file.parent.mkdir(parents=True, exist_ok=True)
        write_config_file.write_text(json.dumps(config, indent=2), encoding="utf-8")
        print(
            f"  {write_config_file.relative_to(project_dir)}  ->  plugin deregistered"
        )


# OpenCode tool.execute.before plugin — fires before every tool call.
# Injects a graph reminder into bash command output when graph.json exists.
_OPENCODE_PLUGIN_JS = """\
// graphify OpenCode plugin
// Injects a knowledge graph reminder before bash tool calls when the graph exists.
import { existsSync } from "fs";
import { join } from "path";

export const GraphifyPlugin = async ({ directory }) => {
  let reminded = false;

  return {
    "tool.execute.before": async (input, output) => {
      if (reminded) return;
      if (!existsSync(join(directory, "graphify-out", "graph.json"))) return;

      if (input.tool === "bash") {
        output.args.command =
          'echo "[graphify] knowledge graph at graphify-out/. For focused questions, run \\`graphify query \\"<question>\\"\\` (scoped subgraph, usually much smaller than GRAPH_REPORT.md) instead of grepping raw files. Read GRAPH_REPORT.md only for broad architecture context." && ' +
          output.args.command;
        reminded = true;
      }
    },
  };
};
"""

_OPENCODE_PLUGIN_PATH = Path(".opencode") / "plugins" / "graphify.js"
_OPENCODE_CONFIG_PATH = Path(".opencode") / "opencode.json"


def _install_opencode_plugin(project_dir: Path) -> None:
    """Write graphify.js plugin and register it in opencode.json."""
    plugin_file = project_dir / _OPENCODE_PLUGIN_PATH
    plugin_file.parent.mkdir(parents=True, exist_ok=True)
    plugin_file.write_text(_OPENCODE_PLUGIN_JS, encoding="utf-8")
    print(f"  {_OPENCODE_PLUGIN_PATH}  ->  tool.execute.before hook written")

    config_file = project_dir / _OPENCODE_CONFIG_PATH
    if config_file.exists():
        try:
            config = json.loads(config_file.read_text(encoding="utf-8"))
        except json.JSONDecodeError:
            config = {}
    else:
        config = {}

    plugins = config.setdefault("plugin", [])
    entry = _OPENCODE_PLUGIN_PATH.as_posix()
    if entry not in plugins:
        plugins.append(entry)
        config_file.write_text(json.dumps(config, indent=2), encoding="utf-8")
        print(f"  {_OPENCODE_CONFIG_PATH}  ->  plugin registered")
    else:
        print(f"  {_OPENCODE_CONFIG_PATH}  ->  plugin already registered (no change)")


def _uninstall_opencode_plugin(project_dir: Path) -> None:
    """Remove graphify.js plugin and deregister from opencode.json."""
    plugin_file = project_dir / _OPENCODE_PLUGIN_PATH
    if plugin_file.exists():
        plugin_file.unlink()
        print(f"  {_OPENCODE_PLUGIN_PATH}  ->  removed")

    config_file = project_dir / _OPENCODE_CONFIG_PATH
    if not config_file.exists():
        return
    try:
        config = json.loads(config_file.read_text(encoding="utf-8"))
    except json.JSONDecodeError:
        return
    plugins = config.get("plugin", [])
    entry = _OPENCODE_PLUGIN_PATH.as_posix()
    if entry in plugins:
        plugins.remove(entry)
        if not plugins:
            config.pop("plugin")
        config_file.write_text(json.dumps(config, indent=2), encoding="utf-8")
        print(f"  {_OPENCODE_CONFIG_PATH}  ->  plugin deregistered")


_CODEX_HOOK = {
    "hooks": {
        "PreToolUse": [
            {
                "matcher": "Bash",
                "hooks": [
                    {
                        "type": "command",
                        # Use the graphify CLI itself so the hook is shell-agnostic:
                        # no [ -f ] bash syntax, no python3 vs python Conda issue,
                        # no JSON escaping inside PowerShell strings. Works on
                        # Windows (PowerShell/cmd.exe), macOS, and Linux.
                        "command": "graphify hook-check",
                    }
                ],
            }
        ]
    }
}


def _resolve_graphify_exe() -> str:
    """Return the absolute path to the graphify executable.

    Falls back to bare 'graphify' if resolution fails. Using an absolute path
    ensures the hook works in environments where the venv Scripts/ directory is
    not on PATH (e.g. VS Code Codex extension on Windows).
    """
    import shutil
    found = shutil.which("graphify")
    if found:
        return found
    # Derive from sys.executable: same Scripts/ (Windows) or bin/ (Unix) dir
    scripts_dir = Path(sys.executable).parent
    for name in ("graphify.exe", "graphify"):
        candidate = scripts_dir / name
        if candidate.exists():
            return str(candidate)
    return "graphify"


def _install_codex_hook(project_dir: Path) -> None:
    """Add graphify PreToolUse hook to .codex/hooks.json."""
    hooks_path = project_dir / ".codex" / "hooks.json"
    hooks_path.parent.mkdir(parents=True, exist_ok=True)

    if hooks_path.exists():
        try:
            existing = json.loads(hooks_path.read_text(encoding="utf-8"))
        except json.JSONDecodeError:
            existing = {}
    else:
        existing = {}

    graphify_exe = _resolve_graphify_exe()
    hook_entry = {
        "hooks": {
            "PreToolUse": [
                {
                    "matcher": "Bash",
                    "hooks": [{"type": "command", "command": f"{graphify_exe} hook-check"}],
                }
            ]
        }
    }

    pre_tool = existing.setdefault("hooks", {}).setdefault("PreToolUse", [])
    existing["hooks"]["PreToolUse"] = [h for h in pre_tool if "graphify" not in str(h)]
    existing["hooks"]["PreToolUse"].extend(hook_entry["hooks"]["PreToolUse"])
    hooks_path.write_text(json.dumps(existing, indent=2), encoding="utf-8")
    print(f"  .codex/hooks.json  ->  PreToolUse hook registered ({graphify_exe} hook-check)")


def _uninstall_codex_hook(project_dir: Path) -> None:
    """Remove graphify PreToolUse hook from .codex/hooks.json."""
    hooks_path = project_dir / ".codex" / "hooks.json"
    if not hooks_path.exists():
        return
    try:
        existing = json.loads(hooks_path.read_text(encoding="utf-8"))
    except json.JSONDecodeError:
        return
    pre_tool = existing.get("hooks", {}).get("PreToolUse", [])
    filtered = [h for h in pre_tool if "graphify" not in str(h)]
    existing["hooks"]["PreToolUse"] = filtered
    hooks_path.write_text(json.dumps(existing, indent=2), encoding="utf-8")
    print(f"  .codex/hooks.json  ->  PreToolUse hook removed")


def _agents_install(project_dir: Path, platform: str) -> None:
    """Write the graphify section to the local AGENTS.md for always-on platforms."""
    target = (project_dir or Path(".")) / "AGENTS.md"

    if target.exists():
        content = target.read_text(encoding="utf-8")
        new_content = _replace_or_append_section(
            content, _AGENTS_MD_MARKER, _always_on("agents-md")
        )
    else:
        new_content = _always_on("agents-md")

    if target.exists() and new_content == target.read_text(encoding="utf-8"):
        print(f"graphify already configured in {target.resolve()} (no change)")
    else:
        target.write_text(new_content, encoding="utf-8")
        print(f"graphify section written to {target.resolve()}")

    if platform == "codex":
        _install_codex_hook(project_dir or Path("."))
    elif platform == "opencode":
        _install_opencode_plugin(project_dir or Path("."))
    elif platform == "kilo":
        _install_kilo_plugin(project_dir or Path("."))

    print()
    print(
        f"{platform.capitalize()} will now check the knowledge graph before answering"
    )
    print("codebase questions and rebuild it after code changes.")
    if platform not in ("codex", "opencode", "kilo"):
        print()
        print("Note: unlike Claude Code, there is no PreToolUse hook equivalent for")
        print(
            f"{platform.capitalize()} — the AGENTS.md rules are the always-on mechanism."
        )


def _amp_legacy_cleanup() -> None:
    """Best-effort removal of the pre-fix ~/.amp/skills/graphify install dir.

    Older graphify versions wrote the Amp skill to ~/.amp/skills, which Amp does
    not search. Clean it up on install so a stale, never-loaded copy does not
    linger. Failures are ignored (the new path is what matters).
    """
    legacy = Path.home() / ".amp" / "skills" / "graphify"
    if legacy.exists():
        shutil.rmtree(legacy, ignore_errors=True)
        if not legacy.exists():
            print(f"  legacy removed   ->  {legacy}")


def _amp_install(project_dir: Path | None = None) -> None:
    """User-scope Amp install: skill into ~/.config/agents/skills + AGENTS.md."""
    _amp_legacy_cleanup()
    _copy_skill_file("amp")
    _agents_install(project_dir or Path("."), "amp")


def _amp_uninstall(project_dir: Path | None = None) -> None:
    """User-scope Amp uninstall: remove the skill and the AGENTS.md section."""
    removed = _remove_skill_file("amp")
    if removed:
        print("skill removed")
    _agents_uninstall(project_dir or Path("."), platform="amp")


def _project_install(platform_name: str, project_dir: Path | None = None) -> None:
    """Install platform skill/config files in the current project."""
    project_dir = project_dir or Path(".")
    if platform_name in ("claude", "windows"):
        install(platform=platform_name, project=True, project_dir=project_dir)
        claude_install(project_dir)
        _print_project_git_add_hint([project_dir / ".claude", project_dir / "CLAUDE.md"])
    elif platform_name == "gemini":
        gemini_install(project_dir, project=True)
    elif platform_name == "cursor":
        _cursor_install(project_dir)
        _print_project_git_add_hint([project_dir / ".cursor"])
    elif platform_name == "kiro":
        _kiro_install(project_dir)
        _print_project_git_add_hint([project_dir / ".kiro"])
    elif platform_name in ("aider", "amp", "codex", "opencode", "claw", "droid", "trae", "trae-cn", "hermes"):
        skill_dst = _copy_skill_file(platform_name, project=True, project_dir=project_dir)
        _agents_install(project_dir, platform_name)
        hint_paths = [_project_scope_root(skill_dst, project_dir), project_dir / "AGENTS.md"]
        if platform_name == "opencode":
            hint_paths.append(project_dir / ".opencode")
        elif platform_name == "codex":
            hint_paths.append(project_dir / ".codex")
        _print_project_git_add_hint(hint_paths)
    elif platform_name == "devin":
        skill_dst = _copy_skill_file("devin", project=True, project_dir=project_dir)
        _devin_rules_install(project_dir)
        _print_project_git_add_hint([_project_scope_root(skill_dst, project_dir), project_dir / ".windsurf"])
    elif platform_name == "antigravity":
        # Project-scoped: skill in .agents/skills/ PLUS the .agents/rules +
        # .agents/workflows always-on layer (previously this path wrote only the
        # skill, leaving the rules/workflows the uninstall path removes unset).
        skill_dst = _copy_skill_file("antigravity", project=True, project_dir=project_dir)
        _antigravity_finalize(skill_dst, project_dir)
        _print_project_git_add_hint([_project_scope_root(skill_dst, project_dir), project_dir / ".agents"])
    elif platform_name in ("copilot", "pi", "kimi"):
        skill_dst = _copy_skill_file(platform_name, project=True, project_dir=project_dir)
        _print_project_git_add_hint([_project_scope_root(skill_dst, project_dir)])
    else:
        install(platform=platform_name, project=True, project_dir=project_dir)


def _project_uninstall(platform_name: str, project_dir: Path | None = None) -> None:
    """Remove project-scoped platform skill/config files only."""
    project_dir = project_dir or Path(".")
    if platform_name in ("claude", "windows"):
        _remove_skill_file(platform_name, project=True, project_dir=project_dir)
        _remove_claude_skill_registration(project_dir)
        claude_uninstall(project_dir, project=True)
    elif platform_name == "gemini":
        gemini_uninstall(project_dir, project=True)
    elif platform_name == "cursor":
        _cursor_uninstall(project_dir)
    elif platform_name == "kiro":
        _kiro_uninstall(project_dir)
    elif platform_name in ("aider", "amp", "codex", "opencode", "claw", "droid", "trae", "trae-cn", "hermes"):
        _remove_skill_file(platform_name, project=True, project_dir=project_dir)
        _agents_uninstall(project_dir, platform=platform_name)
        if platform_name == "codex":
            _uninstall_codex_hook(project_dir)
    elif platform_name == "antigravity":
        _antigravity_uninstall(project_dir, project=True)
    elif platform_name == "devin":
        removed = _remove_skill_file("devin", project=True, project_dir=project_dir)
        _devin_rules_uninstall(project_dir)
        if not removed:
            print("nothing to remove")
    elif platform_name in ("copilot", "pi", "kimi"):
        removed = _remove_skill_file(platform_name, project=True, project_dir=project_dir)
        if not removed:
            print("nothing to remove")
    elif platform_name == "codebuddy":
        codebuddy_uninstall(project_dir)
    else:
        _remove_skill_file(platform_name, project=True, project_dir=project_dir)


def _project_uninstall_all(project_dir: Path | None = None) -> None:
    """Remove project-scoped install files without touching user-scope installs."""
    project_dir = project_dir or Path(".")
    print("Uninstalling project-scoped graphify files...\n")
    for platform_name in _PLATFORM_CONFIG:
        _project_uninstall(platform_name, project_dir)
    for platform_name in ("gemini", "cursor"):
        _project_uninstall(platform_name, project_dir)
    print("\nDone.")


def _agents_uninstall(project_dir: Path, platform: str = "") -> None:
    """Remove the graphify section from the local AGENTS.md."""
    target = (project_dir or Path(".")) / "AGENTS.md"

    if not target.exists():
        print("No AGENTS.md found in current directory - nothing to do")
        if platform == "opencode":
            _uninstall_opencode_plugin(project_dir or Path("."))
        elif platform == "kilo":
            _uninstall_kilo_plugin(project_dir or Path("."))
        return

    content = target.read_text(encoding="utf-8")
    if _AGENTS_MD_MARKER not in content:
        print("graphify section not found in AGENTS.md - nothing to do")
        if platform == "opencode":
            _uninstall_opencode_plugin(project_dir or Path("."))
        elif platform == "kilo":
            _uninstall_kilo_plugin(project_dir or Path("."))
        return

    cleaned = re.sub(
        r"\n*## graphify\n.*?(?=\n## |\Z)",
        "",
        content,
        flags=re.DOTALL,
    ).rstrip()
    if cleaned:
        target.write_text(cleaned + "\n", encoding="utf-8")
        print(f"graphify section removed from {target.resolve()}")
    else:
        target.unlink()
        print(f"AGENTS.md was empty after removal - deleted {target.resolve()}")

    if platform == "opencode":
        _uninstall_opencode_plugin(project_dir or Path("."))
    elif platform == "kilo":
        _uninstall_kilo_plugin(project_dir or Path("."))


def _kilo_uninstall_global() -> list[str]:
    removed = []
    command_dst = Path.home() / ".config" / "kilo" / "command" / "graphify.md"
    if command_dst.exists():
        command_dst.unlink()
        removed.append(f"command removed: {command_dst}")
    try:
        command_dst.parent.rmdir()
    except OSError:
        pass

    skill_dst = Path.home() / _PLATFORM_CONFIG["kilo"]["skill_dst"]
    if skill_dst.exists():
        skill_dst.unlink()
        removed.append(f"skill removed: {skill_dst}")
    version_file = skill_dst.parent / ".graphify_version"
    if version_file.exists():
        version_file.unlink()
    for d in (
        skill_dst.parent,
        skill_dst.parent.parent,
        skill_dst.parent.parent.parent,
    ):
        try:
            d.rmdir()
        except OSError:
            break

    return removed


def _kilo_install(project_dir: Path) -> None:
    """Install native Kilo skill + command globally and always-on project wiring locally."""
    install(platform="kilo")
    _agents_install(project_dir or Path("."), "kilo")


def _kilo_uninstall(project_dir: Path) -> None:
    """Remove Kilo always-on project wiring and global skill/command files."""
    _agents_uninstall(project_dir or Path("."), platform="kilo")
    removed = _kilo_uninstall_global()
    print("; ".join(removed) if removed else "nothing to remove")


def claude_install(project_dir: Path | None = None) -> None:
    """Write the graphify section to the local CLAUDE.md."""
    target = (project_dir or Path(".")) / "CLAUDE.md"

    if target.exists():
        content = target.read_text(encoding="utf-8")
        new_content = _replace_or_append_section(
            content, _CLAUDE_MD_MARKER, _always_on("claude-md")
        )
    else:
        new_content = _always_on("claude-md")

    if target.exists() and new_content == target.read_text(encoding="utf-8"):
        print(f"graphify already configured in {target.resolve()} (no change)")
    else:
        target.write_text(new_content, encoding="utf-8")
        print(f"graphify section written to {target.resolve()}")

    # Always re-install the Claude Code PreToolUse hook so an old hook
    # payload (e.g. pre-issue-#580 wording) is replaced on upgrade.
    _install_claude_hook(project_dir or Path("."))

    print()
    print("Claude Code will now check the knowledge graph before answering")
    print("codebase questions and rebuild it after code changes.")


def _install_claude_hook(project_dir: Path) -> None:
    """Add graphify PreToolUse hook to .claude/settings.json."""
    settings_path = project_dir / ".claude" / "settings.json"
    settings_path.parent.mkdir(parents=True, exist_ok=True)

    if settings_path.exists():
        try:
            settings = json.loads(settings_path.read_text(encoding="utf-8"))
        except json.JSONDecodeError:
            settings = {}
    else:
        settings = {}

    hooks = settings.setdefault("hooks", {})
    pre_tool = hooks.setdefault("PreToolUse", [])

    hooks["PreToolUse"] = [h for h in pre_tool if not (h.get("matcher") in ("Glob|Grep", "Bash", "Read|Glob") and "graphify" in str(h))]
    hooks["PreToolUse"].append(_SETTINGS_HOOK)
    hooks["PreToolUse"].append(_READ_SETTINGS_HOOK)
    settings_path.write_text(json.dumps(settings, indent=2), encoding="utf-8")
    print(f"  .claude/settings.json  ->  PreToolUse hooks registered (Bash search + Read/Glob)")


def _uninstall_claude_hook(project_dir: Path) -> None:
    """Remove graphify PreToolUse hook from .claude/settings.json."""
    settings_path = project_dir / ".claude" / "settings.json"
    if not settings_path.exists():
        return
    try:
        settings = json.loads(settings_path.read_text(encoding="utf-8"))
    except json.JSONDecodeError:
        return
    pre_tool = settings.get("hooks", {}).get("PreToolUse", [])
    filtered = [h for h in pre_tool if not (h.get("matcher") in ("Glob|Grep", "Bash", "Read|Glob") and "graphify" in str(h))]
    if len(filtered) == len(pre_tool):
        return
    settings["hooks"]["PreToolUse"] = filtered
    settings_path.write_text(json.dumps(settings, indent=2), encoding="utf-8")
    print(f"  .claude/settings.json  ->  PreToolUse hook removed")


def uninstall_all(project_dir: Path | None = None, purge: bool = False) -> None:
    """Remove graphify from every platform detected in the current project."""
    pd = project_dir or Path(".")
    print("Uninstalling graphify from all detected platforms...\n")

    # Skill-file / config-section uninstallers
    claude_uninstall(pd)
    codebuddy_uninstall(pd)
    gemini_uninstall(pd)
    vscode_uninstall(pd)
    _cursor_uninstall(pd)
    _kiro_uninstall(pd)
    _antigravity_uninstall(pd)
    # AGENTS.md covers: codex, aider, opencode, claw, droid, trae, trae-cn, hermes, copilot
    _agents_uninstall(pd)
    # Amp also drops a user-scope skill at ~/.config/agents/skills, which the
    # AGENTS.md cleanup above does not touch.
    _remove_skill_file("amp")
    _uninstall_opencode_plugin(pd)
    _uninstall_codex_hook(pd)

    # Git hook
    try:
        from graphify.hooks import uninstall as hook_uninstall
        result = hook_uninstall(pd)
        if result:
            print(result)
    except Exception:
        pass

    if purge:
        import shutil as _shutil
        out = pd / "graphify-out"
        if out.exists():
            _shutil.rmtree(out)
            print(f"\n  graphify-out/  ->  deleted (--purge)")
        else:
            print("\n  graphify-out/  ->  not found (nothing to purge)")

    print("\nDone. Run 'pip uninstall graphifyy' to remove the package itself.")


def claude_uninstall(project_dir: Path | None = None, *, project: bool = False) -> None:
    """Remove the graphify skill tree (SKILL.md + references/) and the CLAUDE.md section.

    Mirrors gemini_uninstall: the bare `graphify uninstall` and `graphify claude
    uninstall` must remove the installed skill, not just strip CLAUDE.md, or the
    progressive-disclosure tree (SKILL.md + references/) is orphaned (#1121).
    """
    project_dir = project_dir or Path(".")
    _remove_skill_file("claude", project=project, project_dir=project_dir)
    target = project_dir / "CLAUDE.md"

    if not target.exists():
        print("No CLAUDE.md found in current directory - nothing to do")
        return

    content = target.read_text(encoding="utf-8")
    if _CLAUDE_MD_MARKER not in content:
        print("graphify section not found in CLAUDE.md - nothing to do")
        return

    # Remove the ## graphify section: from the marker to the next ## heading or EOF
    cleaned = re.sub(
        r"\n*## graphify\n.*?(?=\n## |\Z)",
        "",
        content,
        flags=re.DOTALL,
    ).rstrip()
    if cleaned:
        target.write_text(cleaned + "\n", encoding="utf-8")
        print(f"graphify section removed from {target.resolve()}")
    else:
        target.unlink()
        print(f"CLAUDE.md was empty after removal - deleted {target.resolve()}")

    _uninstall_claude_hook(project_dir or Path("."))


def codebuddy_install(project_dir: Path | None = None) -> None:
    """Write the graphify section to the local CODEBUDDY.md."""
    target = (project_dir or Path(".")) / "CODEBUDDY.md"

    if target.exists():
        content = target.read_text(encoding="utf-8")
        new_content = _replace_or_append_section(
            content, _CODEBUDDY_MD_MARKER, _always_on("claude-md")
        )
    else:
        new_content = _always_on("claude-md")

    if target.exists() and new_content == target.read_text(encoding="utf-8"):
        print(f"graphify already configured in {target.resolve()} (no change)")
    else:
        target.write_text(new_content, encoding="utf-8")
        print(f"graphify section written to {target.resolve()}")

    # Also write CodeBuddy PreToolUse hook to .codebuddy/settings.json
    _install_codebuddy_hook(project_dir or Path("."))

    print()
    print("CodeBuddy will now check the knowledge graph before answering")
    print("codebase questions and rebuild it after code changes.")


def _install_codebuddy_hook(project_dir: Path) -> None:
    """Add graphify PreToolUse hook to .codebuddy/settings.json."""
    settings_path = project_dir / ".codebuddy" / "settings.json"
    settings_path.parent.mkdir(parents=True, exist_ok=True)

    if settings_path.exists():
        try:
            settings = json.loads(settings_path.read_text(encoding="utf-8"))
        except json.JSONDecodeError:
            settings = {}
    else:
        settings = {}

    hooks = settings.setdefault("hooks", {})
    pre_tool = hooks.setdefault("PreToolUse", [])

    hooks["PreToolUse"] = [h for h in pre_tool if not (h.get("matcher") in ("Glob|Grep", "Bash", "Read|Glob") and "graphify" in str(h))]
    hooks["PreToolUse"].append(_SETTINGS_HOOK)
    hooks["PreToolUse"].append(_READ_SETTINGS_HOOK)
    settings_path.write_text(json.dumps(settings, indent=2), encoding="utf-8")
    print(f"  .codebuddy/settings.json  ->  PreToolUse hooks registered")


def _uninstall_codebuddy_hook(project_dir: Path) -> None:
    """Remove graphify PreToolUse hook from .codebuddy/settings.json."""
    settings_path = project_dir / ".codebuddy" / "settings.json"
    if not settings_path.exists():
        return
    try:
        settings = json.loads(settings_path.read_text(encoding="utf-8"))
    except json.JSONDecodeError:
        return
    pre_tool = settings.get("hooks", {}).get("PreToolUse", [])
    filtered = [h for h in pre_tool if not (h.get("matcher") in ("Glob|Grep", "Bash", "Read|Glob") and "graphify" in str(h))]
    if len(filtered) == len(pre_tool):
        return
    settings["hooks"]["PreToolUse"] = filtered
    settings_path.write_text(json.dumps(settings, indent=2), encoding="utf-8")
    print(f"  .codebuddy/settings.json  ->  PreToolUse hook removed")


def codebuddy_uninstall(project_dir: Path | None = None, *, project: bool = False) -> None:
    """Remove the graphify skill tree (SKILL.md + references/) and the CODEBUDDY.md section."""
    project_dir = project_dir or Path(".")
    _remove_skill_file("codebuddy", project=project, project_dir=project_dir)
    target = project_dir / "CODEBUDDY.md"

    if not target.exists():
        print("No CODEBUDDY.md found in current directory - nothing to do")
        return

    content = target.read_text(encoding="utf-8")
    if _CODEBUDDY_MD_MARKER not in content:
        print("graphify section not found in CODEBUDDY.md - nothing to do")
        return

    # Remove the ## graphify section: from the marker to the next ## heading or EOF
    cleaned = re.sub(
        r"\n*## graphify\n.*?(?=\n## |\Z)",
        "",
        content,
        flags=re.DOTALL,
    ).rstrip()
    if cleaned:
        target.write_text(cleaned + "\n", encoding="utf-8")
        print(f"graphify section removed from {target.resolve()}")
    else:
        target.unlink()
        print(f"CODEBUDDY.md was empty after removal - deleted {target.resolve()}")

    _uninstall_codebuddy_hook(project_dir or Path("."))

def _clone_repo(
    url: str, branch: str | None = None, out_dir: Path | None = None
) -> Path:
    """Clone a GitHub repo to a local cache dir and return the path.

    Clones into ~/.graphify/repos/<owner>/<repo> by default so repeated
    runs on the same URL reuse the existing clone (git pull instead of clone).
    """
    import subprocess as _sp
    import re as _re

    # Normalise URL — strip trailing .git if present
    url = url.rstrip("/")
    if not url.endswith(".git"):
        git_url = url + ".git"
    else:
        git_url = url
        url = url[:-4]

    # Extract owner/repo from URL
    m = _re.search(r"github\.com[:/]([^/]+)/([^/]+?)(?:\.git)?$", url)
    if not m:
        print(f"error: not a recognised GitHub URL: {url}", file=sys.stderr)
        sys.exit(1)
    owner, repo = m.group(1), m.group(2)

    if out_dir:
        dest = out_dir
    else:
        dest = Path.home() / ".graphify" / "repos" / owner / repo

    if branch and branch.startswith("-"):
        print(f"error: invalid branch name: {branch!r}", file=sys.stderr)
        sys.exit(1)

    if dest.exists():
        print(f"Repo already cloned at {dest} - pulling latest...", flush=True)
        cmd = ["git", "-C", str(dest), "pull"]
        if branch:
            cmd += ["origin", "--", branch]
        result = _sp.run(cmd, capture_output=True, text=True)
        if result.returncode != 0:
            print(f"warning: git pull failed:\n{result.stderr}", file=sys.stderr)
    else:
        dest.parent.mkdir(parents=True, exist_ok=True)
        print(f"Cloning {url} -> {dest} ...", flush=True)
        cmd = ["git", "clone", "--depth", "1"]
        if branch:
            cmd += ["--branch", branch]
        cmd += ["--", git_url, str(dest)]
        result = _sp.run(cmd, capture_output=True, text=True)
        if result.returncode != 0:
            print(f"error: git clone failed:\n{result.stderr}", file=sys.stderr)
            sys.exit(1)

    print(f"Ready at: {dest}", flush=True)
    return dest


def main() -> None:
    for _stream in (sys.stdout, sys.stderr):
        if _stream is not None and hasattr(_stream, "reconfigure"):
            try:
                _stream.reconfigure(encoding="utf-8", errors="replace")
            except Exception:
                pass
    # Check all known skill install locations for a stale version stamp.
    # Skip during install/uninstall (hook writes trigger a fresh check anyway).
    # Skip during hook-check — it runs on every editor tool use and must be silent.
    # Deduplicate paths so platforms sharing the same install dir don't warn twice.
    _silent_cmds = {"install", "uninstall", "hook-check"}
    if not any(arg in _silent_cmds for arg in sys.argv):
        # Resolve each platform's real user-scope destination so per-platform
        # overrides (gemini, opencode, devin, antigravity, amp) check the dir
        # they actually install into, not the bare cfg['skill_dst'].
        for skill_dst in {_platform_skill_destination(name) for name in _PLATFORM_CONFIG}:
            _check_skill_version(skill_dst)

    if len(sys.argv) >= 2 and sys.argv[1] in ("-v", "--version", "version"):
        print(f"graphify {__version__}")
        return

    if len(sys.argv) < 2 or sys.argv[1] in ("-h", "--help", "-?"):
        print("Usage: graphify <command>")
        print()
        print("Commands:")
        print("  install [--platform P]  copy skill to platform config dir (claude|windows|codebuddy|codex|opencode|aider|amp|claw|droid|trae|trae-cn|gemini|cursor|antigravity|hermes|kiro|pi|devin)")
        print("  uninstall               remove graphify from all detected platforms in one shot")
        print("    --purge                 also delete graphify-out/ directory")
        print("  path \"A\" \"B\"            shortest path between two nodes in graph.json")
        print("    --graph <path>          path to graph.json (default graphify-out/graph.json)")
        print("  explain \"X\"             plain-language explanation of a node and its neighbors")
        print("    --graph <path>          path to graph.json (default graphify-out/graph.json)")
        print("  diagnose multigraph    report same-endpoint edge collapse risk in graph.json")
        print("    --graph <path>          path to graph/extraction JSON")
        print("                            (default graphify-out/graph.json)")
        print("    --json                  emit machine-readable JSON")
        print("    --max-examples N        max same-endpoint examples to print (default 5)")
        print("    --directed              force directed post-build simulation")
        print("    --undirected            force undirected post-build simulation")
        print("                            (default follows JSON directed flag;")
        print("                             raw extraction with no flag defaults directed)")
        print("    --extract-path PATH     extractor source for suppression scan")
        print("  clone <github-url>      clone a GitHub repo locally and print its path for /graphify")
        print("  merge-driver <base> <current> <other>  git merge driver: union-merge two graph.json files (set up via hook install)")
        print("  merge-graphs <g1> <g2>  merge two or more graph.json files into one cross-repo graph")
        print("    --out <path>            output path (default: graphify-out/merged-graph.json)")
        print("    --branch <branch>       checkout a specific branch (default: repo default)")
        print("    --out <dir>             clone to a custom directory (default: ~/.graphify/repos/<owner>/<repo>)")
        print("  add <url>               fetch a URL and save it to ./raw, then update the graph")
        print("    --author \"Name\"         tag the author of the content")
        print("    --contributor \"Name\"    tag who added it to the corpus")
        print("    --dir <path>            target directory (default: ./raw)")
        print("  watch <path>            watch a folder and rebuild the graph on code changes")
        print("  update <path>           re-extract code files and update the graph (no LLM needed)")
        print("    --force                 overwrite graph.json even if the rebuild has fewer nodes")
        print("                            (also: GRAPHIFY_FORCE=1 env var; use after refactors that delete code)")
        print("    --no-cluster            skip clustering, write raw extraction only")
        print("  cluster-only <path>     rerun clustering on an existing graph.json and regenerate report")
        print("    --no-viz                skip graph.html generation (useful for >5000 node graphs / CI)")
        print("    --graph <path>          path to graph.json (default <path>/graphify-out/graph.json)")
        print("    --no-label              keep 'Community N' placeholders (skip LLM community naming)")
        print("    --backend=<name>        backend to use for community naming (default: auto-detect)")
        print("  label <path>            (re)name communities with the configured LLM backend, regenerate report")
        print("    --backend=<name>        backend to use (default: auto-detect from API keys)")
        print("  query \"<question>\"       BFS traversal of graph.json for a question")
        print("    --dfs                   use depth-first instead of breadth-first")
        print("    --context C             explicit edge-context filter (repeatable)")
        print("    --budget N              cap output at N tokens (default 2000)")
        print("    --graph <path>          path to graph.json (default graphify-out/graph.json)")
        print("  affected \"X\"             reverse traversal to find nodes impacted by X")
        print("    --relation R            edge relation to traverse in reverse (repeatable)")
        print("    --depth N               reverse traversal depth (default 2)")
        print("    --graph <path>          path to graph.json (default graphify-out/graph.json)")
        print("  save-result             save a Q&A result to graphify-out/memory/ for graph feedback loop")
        print("    --question Q            the question asked")
        print("    --answer A              the answer to save")
        print(
            "    --type T                query type: query|path_query|explain (default: query)"
        )
        print("    --nodes N1 N2 ...       source node labels cited in the answer")
        print("    --memory-dir DIR        memory directory (default: graphify-out/memory)")
        print("  check-update <path>     check needs_update flag and notify if semantic re-extraction is pending (cron-safe)")
        print("  tree                    emit a D3 v7 collapsible-tree HTML for graph.json")
        print("    --graph PATH            path to graph.json (default graphify-out/graph.json)")
        print("    --output HTML           output path (default graphify-out/GRAPH_TREE.html)")
        print("    --root PATH             filesystem root for the hierarchy")
        print("    --max-children N        cap children per node (default 200)")
        print("    --top-k-edges N         per-symbol outbound edges in inspector (default 12)")
        print("    --label NAME            project label in header")
        print("  extract <path>          headless full extraction (AST + semantic LLM) for CI/scripts")
        print("    --backend B             gemini|kimi|claude|openai|deepseek|ollama (default: whichever API key is set)")
        print("    --model M               override backend default model")
        print("    --mode deep             aggressive INFERRED-edge semantic extraction")
        print("    --max-workers N         AST extraction subprocess count (default: cpu_count)")
        print("    --token-budget N        per-chunk token cap for semantic extraction (default: 60000)")
        print("    --max-concurrency N     parallel semantic chunks in flight (default: 4; set 1 for local LLMs)")
        print("    --api-timeout S         per-request timeout in seconds for the LLM client (default: 600)")
        print("    --out DIR               output dir (default: <path>); writes <DIR>/graphify-out/")
        print("    --google-workspace      export .gdoc/.gsheet/.gslides shortcuts via gws before extraction")
        print("    --no-cluster            skip clustering, write raw extraction only")
        print("    --postgres DSN          extract schema from a live PostgreSQL database")
        print("                            maps tables, views, functions + FK relationships;")
        print("                            column-level detail is not represented in the graph")
        print("    --global                also merge the resulting graph into the global graph")
        print("    --as <tag>              repo tag for --global (default: target directory name)")
        print("  global add <graph.json>  add/update a project graph in the global graph (~/.graphify/global-graph.json)")
        print("    --as <tag>               repo tag (default: parent directory name)")
        print("  global remove <tag>      remove a repo's nodes from the global graph")
        print("  global list              list repos in the global graph")
        print("  global path              print path to the global graph file")
        print("  benchmark [graph.json]  measure token reduction vs naive full-corpus approach")
        print("  export callflow-html    emit Mermaid-based architecture/call-flow HTML")
        print("  hook install            install post-commit/post-checkout git hooks (all platforms)")
        print("  hook uninstall          remove git hooks")
        print("  hook status             check if git hooks are installed")
        print(
            "  gemini install          write GEMINI.md section + BeforeTool hook (Gemini CLI)"
        )
        print("  gemini uninstall        remove GEMINI.md section + BeforeTool hook")
        print("  cursor install          write .cursor/rules/graphify.mdc (Cursor)")
        print("  cursor uninstall        remove .cursor/rules/graphify.mdc")
        print("  claude install          write graphify section to CLAUDE.md + PreToolUse hook (Claude Code)")
        print("  claude uninstall        remove graphify section from CLAUDE.md + PreToolUse hook")
        print("  codebuddy install       write graphify section to CODEBUDDY.md + PreToolUse hook (CodeBuddy)")
        print("  codebuddy uninstall     remove graphify section from CODEBUDDY.md + PreToolUse hook")
        print("  codex install           write graphify section to AGENTS.md (Codex)")
        print("  codex uninstall         remove graphify section from AGENTS.md")
        print(
            "  opencode install        write graphify section to AGENTS.md + tool.execute.before plugin (OpenCode)"
        )
        print(
            "  opencode uninstall      remove graphify section from AGENTS.md + plugin"
        )
        print(
            "  kilo install            install native Kilo skill + command + AGENTS.md + .kilo plugin"
        )
        print(
            "  kilo uninstall          remove native Kilo skill + command + AGENTS.md + .kilo plugin"
        )
        print("  aider install           write graphify section to AGENTS.md (Aider)")
        print("  aider uninstall         remove graphify section from AGENTS.md")
        print(
            "  copilot install         copy graphify skill to ~/.copilot/skills (GitHub Copilot CLI)"
        )
        print("  copilot uninstall       remove graphify skill from ~/.copilot/skills")
        print(
            "  vscode install          configure VS Code Copilot Chat (skill + .github/copilot-instructions.md)"
        )
        print("  vscode uninstall        remove VS Code Copilot Chat configuration")
        print(
            "  claw install            write graphify section to AGENTS.md (OpenClaw)"
        )
        print("  claw uninstall          remove graphify section from AGENTS.md")
        print(
            "  droid install           write graphify section to AGENTS.md (Factory Droid)"
        )
        print("  droid uninstall        remove graphify section from AGENTS.md")
        print("  trae install            write graphify section to AGENTS.md (Trae)")
        print("  trae uninstall         remove graphify section from AGENTS.md")
        print("  trae-cn install         write graphify section to AGENTS.md (Trae CN)")
        print("  trae-cn uninstall      remove graphify section from AGENTS.md")
        print(
            "  antigravity install     write .agents/rules + .agents/workflows + skill (Google Antigravity)"
        )
        print(
            "  antigravity uninstall   remove .agents/rules, .agents/workflows, and skill"
        )
        print(
            "  hermes install          write skill to ~/.hermes/skills/graphify/ (Hermes)"
        )
        print("  hermes uninstall        remove skill from ~/.hermes/skills/graphify/")
        print(
            "  kiro install            write skill to .kiro/skills/graphify/ + steering file (Kiro IDE/CLI)"
        )
        print("  kiro uninstall          remove skill + steering file")
        print("  pi install              write skill to ~/.pi/agent/skills/graphify/ (Pi coding agent)")
        print("  pi uninstall            remove skill from ~/.pi/agent/skills/graphify/")
        print("  devin install           write skill to ~/.config/devin/skills/graphify/ (Devin CLI)")
        print("  devin uninstall         remove skill from ~/.config/devin/skills/graphify/")
        print()
        return

    cmd = sys.argv[1]

    # Universal help guard: -h/--help/-? anywhere after the command shows help
    # and stops — prevents flags from silently triggering destructive subcommands
    # (e.g. "cursor install --help" was silently installing into Cursor, #821).
    # Exempt: free-text commands (user string may contain these tokens), and
    # "install"/"uninstall" which have their own per-subcommand help handlers.
    _FREE_TEXT_CMDS = {"query", "explain", "path", "save-result", "install", "uninstall"}
    if cmd not in _FREE_TEXT_CMDS and any(a in {"-h", "--help", "-?"} for a in sys.argv[2:]):
        print(f"Run 'graphify --help' for full usage.")
        return

    if cmd == "install":
        # Default to windows platform on Windows, claude elsewhere
        default_platform = "windows" if platform.system() == "Windows" else "claude"
        selected_platform: str | None = None
        project_scope = False
        args = sys.argv[2:]
        i = 0
        while i < len(args):
            arg = args[i]
            if arg in ("-h", "--help"):
                _print_install_usage()
                return
            if arg == "--project":
                project_scope = True
                i += 1
            elif arg.startswith("--platform="):
                candidate = arg.split("=", 1)[1]
                if selected_platform and selected_platform != candidate:
                    print("error: specify install platform only once", file=sys.stderr)
                    sys.exit(1)
                selected_platform = candidate
                i += 1
            elif arg == "--platform":
                if i + 1 >= len(args):
                    print("error: --platform requires a value", file=sys.stderr)
                    sys.exit(1)
                candidate = args[i + 1]
                if selected_platform and selected_platform != candidate:
                    print("error: specify install platform only once", file=sys.stderr)
                    sys.exit(1)
                selected_platform = candidate
                i += 2
            elif arg.startswith("-"):
                print(f"error: unknown install option '{arg}'", file=sys.stderr)
                sys.exit(1)
            else:
                if selected_platform and selected_platform != arg:
                    print("error: specify install platform only once", file=sys.stderr)
                    sys.exit(1)
                selected_platform = arg
                i += 1
        chosen_platform = selected_platform or default_platform
        if project_scope:
            _project_install(chosen_platform, Path("."))
        else:
            install(platform=chosen_platform)
    elif cmd == "uninstall":
        args = sys.argv[2:]
        purge = "--purge" in args
        project_scope = "--project" in args
        selected_platform = None
        i = 0
        while i < len(args):
            arg = args[i]
            if arg in ("--purge", "--project"):
                i += 1
            elif arg.startswith("--platform="):
                selected_platform = arg.split("=", 1)[1]
                i += 1
            elif arg == "--platform":
                if i + 1 >= len(args):
                    print("error: --platform requires a value", file=sys.stderr)
                    sys.exit(1)
                selected_platform = args[i + 1]
                i += 2
            elif arg.startswith("-"):
                print(f"error: unknown uninstall option '{arg}'", file=sys.stderr)
                sys.exit(1)
            else:
                selected_platform = arg
                i += 1
        if project_scope:
            if selected_platform:
                _project_uninstall(selected_platform, Path("."))
            else:
                _project_uninstall_all(Path("."))
        else:
            uninstall_all(purge=purge)
    elif cmd == "claude":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd == "install":
            if "--project" in sys.argv[3:]:
                _project_install("claude", Path("."))
            else:
                claude_install()
        elif subcmd == "uninstall":
            if "--project" in sys.argv[3:]:
                _project_uninstall("claude", Path("."))
            else:
                claude_uninstall()
        else:
            print("Usage: graphify claude [install|uninstall]", file=sys.stderr)
            sys.exit(1)
    elif cmd == "codebuddy":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd == "install":
            codebuddy_install()
        elif subcmd == "uninstall":
            codebuddy_uninstall()
        else:
            print("Usage: graphify codebuddy [install|uninstall]", file=sys.stderr)
            sys.exit(1)
    elif cmd == "gemini":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd == "install":
            gemini_install(project=("--project" in sys.argv[3:]))
        elif subcmd == "uninstall":
            gemini_uninstall(project=("--project" in sys.argv[3:]))
        else:
            print("Usage: graphify gemini [install|uninstall]", file=sys.stderr)
            sys.exit(1)
    elif cmd == "cursor":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd == "install":
            _cursor_install(Path("."))
        elif subcmd == "uninstall":
            _cursor_uninstall(Path("."))
        else:
            print("Usage: graphify cursor [install|uninstall]", file=sys.stderr)
            sys.exit(1)
    elif cmd == "vscode":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd == "install":
            vscode_install()
        elif subcmd == "uninstall":
            vscode_uninstall()
        else:
            print("Usage: graphify vscode [install|uninstall]", file=sys.stderr)
            sys.exit(1)
    elif cmd == "copilot":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd == "install":
            if "--project" in sys.argv[3:]:
                _project_install("copilot", Path("."))
            else:
                install(platform="copilot")
        elif subcmd == "uninstall":
            if "--project" in sys.argv[3:]:
                _project_uninstall("copilot", Path("."))
            else:
                removed = _remove_skill_file("copilot")
                print("skill removed" if removed else "nothing to remove")
        else:
            print("Usage: graphify copilot [install|uninstall]", file=sys.stderr)
            sys.exit(1)
    elif cmd == "kilo":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd == "install":
            _kilo_install(Path("."))
        elif subcmd == "uninstall":
            _kilo_uninstall(Path("."))
        else:
            print("Usage: graphify kilo [install|uninstall]", file=sys.stderr)
            sys.exit(1)
    elif cmd == "kiro":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd == "install":
            _kiro_install(Path("."))
        elif subcmd == "uninstall":
            _kiro_uninstall(Path("."))
        else:
            print("Usage: graphify kiro [install|uninstall]", file=sys.stderr)
            sys.exit(1)
    elif cmd == "devin":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd == "install":
            if "--project" in sys.argv[3:]:
                _project_install("devin", Path("."))
            else:
                install(platform="devin")
        elif subcmd == "uninstall":
            if "--project" in sys.argv[3:]:
                _project_uninstall("devin", Path("."))
            else:
                removed = _remove_skill_file("devin")
                print("skill removed" if removed else "nothing to remove")
        else:
            print("Usage: graphify devin [install|uninstall]", file=sys.stderr)
            sys.exit(1)
    elif cmd == "pi":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd == "install":
            if "--project" in sys.argv[3:]:
                _project_install("pi", Path("."))
            else:
                install("pi")
        elif subcmd == "uninstall":
            if "--project" in sys.argv[3:]:
                _project_uninstall("pi", Path("."))
            else:
                _remove_skill_file("pi")
        else:
            print("Usage: graphify pi [install|uninstall]", file=sys.stderr)
            sys.exit(1)
    elif cmd == "amp":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd == "install":
            if "--project" in sys.argv[3:]:
                _project_install("amp", Path("."))
            else:
                _amp_install(Path("."))
        elif subcmd == "uninstall":
            if "--project" in sys.argv[3:]:
                _project_uninstall("amp", Path("."))
            else:
                _amp_uninstall(Path("."))
        else:
            print("Usage: graphify amp [install|uninstall]", file=sys.stderr)
            sys.exit(1)
    elif cmd in ("aider", "codex", "opencode", "claw", "droid", "trae", "trae-cn", "hermes"):
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd == "install":
            if "--project" in sys.argv[3:]:
                _project_install(cmd, Path("."))
            else:
                _agents_install(Path("."), cmd)
        elif subcmd == "uninstall":
            if "--project" in sys.argv[3:]:
                _project_uninstall(cmd, Path("."))
            else:
                _agents_uninstall(Path("."), platform=cmd)
                if cmd == "codex":
                    _uninstall_codex_hook(Path("."))
        else:
            print(f"Usage: graphify {cmd} [install|uninstall]", file=sys.stderr)
            sys.exit(1)
    elif cmd == "antigravity":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd == "install":
            if "--project" in sys.argv[3:]:
                _project_install("antigravity", Path("."))
            else:
                _antigravity_install(Path("."))
        elif subcmd == "uninstall":
            if "--project" in sys.argv[3:]:
                _project_uninstall("antigravity", Path("."))
            else:
                _antigravity_uninstall(Path("."))
        else:
            print("Usage: graphify antigravity [install|uninstall]", file=sys.stderr)
            sys.exit(1)
    elif cmd == "provider":
        from graphify.llm import _custom_providers_path, BACKENDS
        import json as _json
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        global_path = _custom_providers_path(global_=True)

        if subcmd == "list":
            global_path.parent.mkdir(parents=True, exist_ok=True)
            existing: dict = {}
            if global_path.is_file():
                try:
                    existing = _json.loads(global_path.read_text(encoding="utf-8"))
                except Exception:
                    pass
            if not existing:
                print("No custom providers registered.")
            else:
                for name in existing:
                    print(f"  {name}  ({existing[name].get('base_url', '')})")

        elif subcmd == "show":
            name = sys.argv[3] if len(sys.argv) > 3 else ""
            if not name:
                print("Usage: graphify provider show <name>", file=sys.stderr)
                sys.exit(1)
            existing = {}
            if global_path.is_file():
                try:
                    existing = _json.loads(global_path.read_text(encoding="utf-8"))
                except Exception:
                    pass
            if name not in existing:
                print(f"Provider '{name}' not found.", file=sys.stderr)
                sys.exit(1)
            print(_json.dumps({name: existing[name]}, indent=2))

        elif subcmd == "add":
            args = sys.argv[3:]
            name = args[0] if args and not args[0].startswith("-") else ""
            if not name:
                print("Usage: graphify provider add <name> --base-url URL --default-model MODEL --env-key KEY", file=sys.stderr)
                sys.exit(1)
            if name in BACKENDS:
                print(f"Error: '{name}' is a built-in provider and cannot be overridden.", file=sys.stderr)
                sys.exit(1)
            base_url = ""
            default_model = ""
            env_key = ""
            pricing_input = 0.0
            pricing_output = 0.0
            i = 1
            while i < len(args):
                a = args[i]
                if a == "--base-url" and i + 1 < len(args):
                    base_url = args[i + 1]; i += 2
                elif a.startswith("--base-url="):
                    base_url = a.split("=", 1)[1]; i += 1
                elif a == "--default-model" and i + 1 < len(args):
                    default_model = args[i + 1]; i += 2
                elif a.startswith("--default-model="):
                    default_model = a.split("=", 1)[1]; i += 1
                elif a == "--env-key" and i + 1 < len(args):
                    env_key = args[i + 1]; i += 2
                elif a.startswith("--env-key="):
                    env_key = a.split("=", 1)[1]; i += 1
                elif a == "--pricing-input" and i + 1 < len(args):
                    pricing_input = float(args[i + 1]); i += 2
                elif a == "--pricing-output" and i + 1 < len(args):
                    pricing_output = float(args[i + 1]); i += 2
                else:
                    i += 1
            if not base_url or not default_model or not env_key:
                print("Error: --base-url, --default-model, and --env-key are required.", file=sys.stderr)
                sys.exit(1)
            from graphify.llm import provider_base_url_ok
            if not provider_base_url_ok(base_url, name):
                print(f"Error: refusing to add provider with unsafe base_url {base_url!r}.", file=sys.stderr)
                sys.exit(1)
            global_path.parent.mkdir(parents=True, exist_ok=True)
            existing = {}
            if global_path.is_file():
                try:
                    existing = _json.loads(global_path.read_text(encoding="utf-8"))
                except Exception:
                    pass
            existing[name] = {
                "base_url": base_url,
                "default_model": default_model,
                "env_key": env_key,
                "pricing": {"input": pricing_input, "output": pricing_output},
                "temperature": 0,
            }
            global_path.write_text(_json.dumps(existing, indent=2) + "\n", encoding="utf-8")
            print(f"Provider '{name}' added. Use with: graphify extract . --backend {name}")

        elif subcmd == "remove":
            name = sys.argv[3] if len(sys.argv) > 3 else ""
            if not name:
                print("Usage: graphify provider remove <name>", file=sys.stderr)
                sys.exit(1)
            existing = {}
            if global_path.is_file():
                try:
                    existing = _json.loads(global_path.read_text(encoding="utf-8"))
                except Exception:
                    pass
            if name not in existing:
                print(f"Provider '{name}' not found.", file=sys.stderr)
                sys.exit(1)
            del existing[name]
            global_path.write_text(_json.dumps(existing, indent=2) + "\n", encoding="utf-8")
            print(f"Provider '{name}' removed.")

        else:
            print("Usage: graphify provider [add|list|show|remove]", file=sys.stderr)
            if subcmd:
                sys.exit(1)
    elif cmd == "prs":
        from graphify.prs import cmd_prs
        cmd_prs(sys.argv[2:])
    elif cmd == "hook":
        from graphify.hooks import (
            install as hook_install,
            uninstall as hook_uninstall,
            status as hook_status,
        )

        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd == "install":
            print(hook_install(Path(".")))
        elif subcmd == "uninstall":
            print(hook_uninstall(Path(".")))
        elif subcmd == "status":
            print(hook_status(Path(".")))
        else:
            print("Usage: graphify hook [install|uninstall|status]", file=sys.stderr)
            sys.exit(1)
    elif cmd == "query":
        if len(sys.argv) < 3:
            print("Usage: graphify query \"<question>\" [--dfs] [--context C] [--budget N] [--graph path]", file=sys.stderr)
            sys.exit(1)
        from graphify.serve import _query_graph_text
        from graphify.security import sanitize_label
        from networkx.readwrite import json_graph
        from graphify import querylog

        question = sys.argv[2]
        use_dfs = "--dfs" in sys.argv
        budget = 2000
        graph_path = _default_graph_path()
        context_filters: list[str] = []
        args = sys.argv[3:]
        i = 0
        while i < len(args):
            if args[i] == "--budget" and i + 1 < len(args):
                try:
                    budget = int(args[i + 1])
                except ValueError:
                    print(f"error: --budget must be an integer", file=sys.stderr)
                    sys.exit(1)
                i += 2
            elif args[i].startswith("--budget="):
                try:
                    budget = int(args[i].split("=", 1)[1])
                except ValueError:
                    print(f"error: --budget must be an integer", file=sys.stderr)
                    sys.exit(1)
                i += 1
            elif args[i] == "--context" and i + 1 < len(args):
                context_filters.append(args[i + 1])
                i += 2
            elif args[i].startswith("--context="):
                context_filters.append(args[i].split("=", 1)[1])
                i += 1
            elif args[i] == "--graph" and i + 1 < len(args):
                graph_path = args[i + 1]
                i += 2
            else:
                i += 1
        gp = Path(graph_path).resolve()
        if not gp.exists():
            print(f"error: graph file not found: {gp}", file=sys.stderr)
            sys.exit(1)
        if not gp.suffix == ".json":
            print(f"error: graph file must be a .json file", file=sys.stderr)
            sys.exit(1)
        _enforce_graph_size_cap_or_exit(gp)
        try:
            import json as _json
            import networkx as _nx

            _raw = _json.loads(gp.read_text(encoding="utf-8"))
            if "links" not in _raw and "edges" in _raw:
                _raw = dict(_raw, links=_raw["edges"])
            try:
                G = json_graph.node_link_graph(_raw, edges="links")
            except TypeError:
                G = json_graph.node_link_graph(_raw)
        except Exception as exc:
            print(f"error: could not load graph: {exc}", file=sys.stderr)
            sys.exit(1)
        import time as _time
        _t0 = _time.perf_counter()
        _mode = "dfs" if use_dfs else "bfs"
        _result = _query_graph_text(
            G,
            question,
            mode=_mode,
            depth=2,
            token_budget=budget,
            context_filters=context_filters,
        )
        querylog.log_query(
            kind="query",
            question=question,
            corpus=str(gp),
            result=_result,
            mode=_mode,
            depth=2,
            token_budget=budget,
            duration_ms=(_time.perf_counter() - _t0) * 1000,
        )
        print(_result)
    elif cmd == "affected":
        if len(sys.argv) < 3:
            print("Usage: graphify affected \"<node-or-label>\" [--relation R] [--depth N] [--graph path]", file=sys.stderr)
            sys.exit(1)
        from graphify.affected import DEFAULT_AFFECTED_RELATIONS, format_affected, load_graph
        query = sys.argv[2]
        graph_path = "graphify-out/graph.json"
        depth = 2
        relations: list[str] = []
        args = sys.argv[3:]
        i = 0
        while i < len(args):
            if args[i] == "--graph" and i + 1 < len(args):
                graph_path = args[i + 1]
                i += 2
            elif args[i].startswith("--graph="):
                graph_path = args[i].split("=", 1)[1]
                i += 1
            elif args[i] == "--depth" and i + 1 < len(args):
                try:
                    depth = int(args[i + 1])
                except ValueError:
                    print("error: --depth must be an integer", file=sys.stderr)
                    sys.exit(1)
                i += 2
            elif args[i].startswith("--depth="):
                try:
                    depth = int(args[i].split("=", 1)[1])
                except ValueError:
                    print("error: --depth must be an integer", file=sys.stderr)
                    sys.exit(1)
                i += 1
            elif args[i] == "--relation" and i + 1 < len(args):
                relations.append(args[i + 1])
                i += 2
            elif args[i].startswith("--relation="):
                relations.append(args[i].split("=", 1)[1])
                i += 1
            else:
                i += 1
        gp = Path(graph_path).resolve()
        if not gp.exists():
            print(f"error: graph file not found: {gp}", file=sys.stderr)
            sys.exit(1)
        if not gp.suffix == ".json":
            print("error: graph file must be a .json file", file=sys.stderr)
            sys.exit(1)
        try:
            graph = load_graph(gp)
        except Exception as exc:
            print(f"error: could not load graph: {exc}", file=sys.stderr)
            sys.exit(1)
        print(
            format_affected(
                graph,
                query,
                relations=relations or DEFAULT_AFFECTED_RELATIONS,
                depth=depth,
            )
        )
    elif cmd == "save-result":
        # graphify save-result --question Q --answer A --type T [--nodes N1 N2 ...]
        import argparse as _ap

        p = _ap.ArgumentParser(prog="graphify save-result")
        p.add_argument("--question", required=True)
        p.add_argument("--answer", required=True)
        p.add_argument("--type", dest="query_type", default="query")
        p.add_argument("--nodes", nargs="*", default=[])
        p.add_argument("--memory-dir", default="graphify-out/memory")
        opts = p.parse_args(sys.argv[2:])
        from graphify.ingest import save_query_result as _sqr

        out = _sqr(
            question=opts.question,
            answer=opts.answer,
            memory_dir=Path(opts.memory_dir),
            query_type=opts.query_type,
            source_nodes=opts.nodes or None,
        )
        print(f"Saved to {out}")
    elif cmd == "path":
        if len(sys.argv) < 4:
            print(
                'Usage: graphify path "<source>" "<target>" [--graph path]',
                file=sys.stderr,
            )
            sys.exit(1)
        from graphify.serve import _score_nodes
        from networkx.readwrite import json_graph
        import networkx as _nx

        source_label = sys.argv[2]
        target_label = sys.argv[3]
        graph_path = _default_graph_path()
        args = sys.argv[4:]
        for i, a in enumerate(args):
            if a == "--graph" and i + 1 < len(args):
                graph_path = args[i + 1]
        gp = Path(graph_path).resolve()
        if not gp.exists():
            print(f"error: graph file not found: {gp}", file=sys.stderr)
            sys.exit(1)
        _enforce_graph_size_cap_or_exit(gp)
        _raw = json.loads(gp.read_text(encoding="utf-8"))
        if "links" not in _raw and "edges" in _raw:
            _raw = dict(_raw, links=_raw["edges"])
        # Force directed so the renderer can recover stored caller→callee direction.
        _raw = {**_raw, "directed": True}
        try:
            G = json_graph.node_link_graph(_raw, edges="links")
        except TypeError:
            G = json_graph.node_link_graph(_raw)
        src_scored = _score_nodes(G, [t.lower() for t in source_label.split()])
        tgt_scored = _score_nodes(G, [t.lower() for t in target_label.split()])
        if not src_scored:
            print(f"No node matching '{source_label}' found.", file=sys.stderr)
            sys.exit(1)
        if not tgt_scored:
            print(f"No node matching '{target_label}' found.", file=sys.stderr)
            sys.exit(1)
        src_nid, tgt_nid = src_scored[0][1], tgt_scored[0][1]
        # Ambiguity guard: when both queries resolve to the same node, the
        # shortest path is trivially zero hops, which is almost never what the
        # caller wanted (see bug #828).
        if src_nid == tgt_nid:
            print(
                f"'{source_label}' and '{target_label}' both resolved to the same "
                f"node '{src_nid}'. Use a more specific label or the exact node ID.",
                file=sys.stderr,
            )
            sys.exit(1)
        for _name, _scored in (("source", src_scored), ("target", tgt_scored)):
            if len(_scored) >= 2:
                _top, _runner = _scored[0][0], _scored[1][0]
                if _top > 0 and (_top - _runner) / _top < 0.10:
                    print(
                        f"warning: {_name} match was ambiguous "
                        f"(top score {_top:g}, runner-up {_runner:g})",
                        file=sys.stderr,
                    )
        try:
            path_nodes = _nx.shortest_path(G.to_undirected(as_view=True), src_nid, tgt_nid)
        except (_nx.NetworkXNoPath, _nx.NodeNotFound):
            print(f"No path found between '{source_label}' and '{target_label}'.")
            sys.exit(0)
        hops = len(path_nodes) - 1
        segments = []
        from graphify.build import edge_data
        for i in range(len(path_nodes) - 1):
            u, v = path_nodes[i], path_nodes[i + 1]
            # Check which direction the stored edge points.
            if G.has_edge(u, v):
                edata = edge_data(G, u, v)
                forward = True
            else:
                edata = edge_data(G, v, u)
                forward = False
            rel = edata.get("relation", "")
            conf = edata.get("confidence", "")
            conf_str = f" [{conf}]" if conf else ""
            if i == 0:
                segments.append(G.nodes[u].get("label", u))
            if forward:
                segments.append(f"--{rel}{conf_str}--> {G.nodes[v].get('label', v)}")
            else:
                segments.append(f"<--{rel}{conf_str}-- {G.nodes[v].get('label', v)}")
        print(f"Shortest path ({hops} hops):\n  " + " ".join(segments))
        from graphify import querylog
        querylog.log_query(
            kind="path",
            question=f"{sys.argv[2]} -> {sys.argv[3]}",
            corpus=str(gp),
            nodes_returned=hops,
        )

    elif cmd == "explain":
        if len(sys.argv) < 3:
            print('Usage: graphify explain "<node>" [--graph path]', file=sys.stderr)
            sys.exit(1)
        from graphify.serve import _find_node
        from networkx.readwrite import json_graph

        label = sys.argv[2]
        graph_path = _default_graph_path()
        args = sys.argv[3:]
        for i, a in enumerate(args):
            if a == "--graph" and i + 1 < len(args):
                graph_path = args[i + 1]
        gp = Path(graph_path).resolve()
        if not gp.exists():
            print(f"error: graph file not found: {gp}", file=sys.stderr)
            sys.exit(1)
        _enforce_graph_size_cap_or_exit(gp)
        _raw = json.loads(gp.read_text(encoding="utf-8"))
        if "links" not in _raw and "edges" in _raw:
            _raw = dict(_raw, links=_raw["edges"])
        # Force directed so the renderer can recover stored caller→callee direction.
        _raw = {**_raw, "directed": True}
        try:
            G = json_graph.node_link_graph(_raw, edges="links")
        except TypeError:
            G = json_graph.node_link_graph(_raw)
        matches = _find_node(G, label)
        if not matches:
            print(f"No node matching '{label}' found.")
            sys.exit(0)
        nid = matches[0]
        d = G.nodes[nid]
        print(f"Node: {d.get('label', nid)}")
        print(f"  ID:        {nid}")
        print(
            f"  Source:    {d.get('source_file', '')} {d.get('source_location', '')}".rstrip()
        )
        print(f"  Type:      {d.get('file_type', '')}")
        print(f"  Community: {d.get('community', '')}")
        print(f"  Degree:    {G.degree(nid)}")
        from graphify.build import edge_data
        connections: list[tuple[str, str, dict]] = []  # (direction, neighbor_id, edge_data)
        for nb in G.successors(nid):
            connections.append(("out", nb, edge_data(G, nid, nb)))
        for nb in G.predecessors(nid):
            connections.append(("in", nb, edge_data(G, nb, nid)))
        if connections:
            print(f"\nConnections ({len(connections)}):")
            connections.sort(key=lambda c: G.degree(c[1]), reverse=True)
            for direction, nb, edata in connections[:20]:
                rel = edata.get("relation", "")
                conf = edata.get("confidence", "")
                arrow = "-->" if direction == "out" else "<--"
                print(f"  {arrow} {G.nodes[nb].get('label', nb)} [{rel}] [{conf}]")
            if len(connections) > 20:
                print(f"  ... and {len(connections) - 20} more")
        from graphify import querylog
        querylog.log_query(
            kind="explain",
            question=sys.argv[2],
            corpus=str(gp),
            nodes_returned=len(connections),
        )

    elif cmd == "diagnose":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd != "multigraph":
            print(
                "Usage: graphify diagnose multigraph "
                "[--graph path] [--json] [--max-examples N] "
                "[--directed] [--undirected] [--extract-path path]",
                file=sys.stderr,
            )
            sys.exit(1)

        graph_path = Path(_default_graph_path())
        max_examples = 5
        directed: bool | None = None
        direction_flag: str | None = None
        json_output = False
        extract_path: Path | None = None

        i = 3
        while i < len(sys.argv):
            arg = sys.argv[i]
            if arg == "--graph":
                i += 1
                if i >= len(sys.argv):
                    print("error: --graph requires a path", file=sys.stderr)
                    sys.exit(1)
                graph_path = Path(sys.argv[i])
            elif arg == "--json":
                json_output = True
            elif arg == "--max-examples":
                i += 1
                if i >= len(sys.argv):
                    print("error: --max-examples requires an integer", file=sys.stderr)
                    sys.exit(1)
                try:
                    max_examples = int(sys.argv[i])
                except ValueError:
                    print("error: --max-examples requires an integer", file=sys.stderr)
                    sys.exit(1)
                if max_examples < 0:
                    print("error: --max-examples must be >= 0", file=sys.stderr)
                    sys.exit(1)
            elif arg == "--directed":
                if direction_flag == "undirected":
                    print(
                        "error: --directed and --undirected are mutually exclusive",
                        file=sys.stderr,
                    )
                    sys.exit(1)
                direction_flag = "directed"
                directed = True
            elif arg == "--undirected":
                if direction_flag == "directed":
                    print(
                        "error: --directed and --undirected are mutually exclusive",
                        file=sys.stderr,
                    )
                    sys.exit(1)
                direction_flag = "undirected"
                directed = False
            elif arg == "--extract-path":
                i += 1
                if i >= len(sys.argv):
                    print("error: --extract-path requires a path", file=sys.stderr)
                    sys.exit(1)
                extract_path = Path(sys.argv[i])
            else:
                print(f"error: unknown diagnose option {arg}", file=sys.stderr)
                sys.exit(1)
            i += 1

        from graphify.diagnostics import (
            diagnose_file,
            format_diagnostic_json,
            format_diagnostic_report,
        )

        try:
            summary = diagnose_file(
                graph_path,
                directed=directed,
                root=Path(".").resolve(),
                max_examples=max_examples,
                extract_path=extract_path,
            )
        except Exception as exc:
            print(f"error: {exc}", file=sys.stderr)
            sys.exit(1)

        if json_output:
            print(json.dumps(format_diagnostic_json(summary), indent=2))
        else:
            print(format_diagnostic_report(summary))

    elif cmd == "add":
        if len(sys.argv) < 3:
            print(
                "Usage: graphify add <url> [--author Name] [--contributor Name] [--dir ./raw]",
                file=sys.stderr,
            )
            sys.exit(1)
        from graphify.ingest import ingest as _ingest

        url = sys.argv[2]
        author: str | None = None
        contributor: str | None = None
        target_dir = Path("raw")
        args = sys.argv[3:]
        i = 0
        while i < len(args):
            if args[i] == "--author" and i + 1 < len(args):
                author = args[i + 1]
                i += 2
            elif args[i] == "--contributor" and i + 1 < len(args):
                contributor = args[i + 1]
                i += 2
            elif args[i] == "--dir" and i + 1 < len(args):
                target_dir = Path(args[i + 1])
                i += 2
            else:
                i += 1
        try:
            saved = _ingest(url, target_dir, author=author, contributor=contributor)
            print(f"Saved to {saved}")
            print("Run /graphify --update in your AI assistant to update the graph.")
        except Exception as exc:
            print(f"error: {exc}", file=sys.stderr)
            sys.exit(1)

    elif cmd == "watch":
        watch_path = Path(sys.argv[2]) if len(sys.argv) > 2 else Path(".")
        if not watch_path.exists():
            print(f"error: path not found: {watch_path}", file=sys.stderr)
            sys.exit(1)
        from graphify.watch import watch as _watch

        try:
            _watch(watch_path)
        except ImportError as exc:
            print(f"error: {exc}", file=sys.stderr)
            sys.exit(1)

    elif cmd in ("cluster-only", "label"):
        # `label` is `cluster-only` that always (re)generates community names with
        # the configured backend, even when a .graphify_labels.json already exists.
        force_relabel = cmd == "label"
        # Mirror the tree/export arg-parsing pattern: walk argv so flags and
        # the optional positional path can appear in any order (#724).
        no_viz = "--no-viz" in sys.argv
        no_label = "--no-label" in sys.argv
        _backend_arg = next((a for a in sys.argv if a.startswith("--backend=")), None)
        label_backend = _backend_arg.split("=", 1)[1] if _backend_arg else None
        _min_cs_arg = next((a for a in sys.argv if a.startswith("--min-community-size=")), None)
        min_community_size = int(_min_cs_arg.split("=")[1]) if _min_cs_arg else 3
        args = sys.argv[2:]
        watch_path: Path | None = None
        graph_override: Path | None = None
        co_resolution: float = 1.0
        co_exclude_hubs: float | None = None
        i_arg = 0
        while i_arg < len(args):
            a = args[i_arg]
            if a == "--graph" and i_arg + 1 < len(args):
                graph_override = Path(args[i_arg + 1]); i_arg += 2
            elif a == "--resolution" and i_arg + 1 < len(args):
                co_resolution = float(args[i_arg + 1]); i_arg += 2
            elif a.startswith("--resolution="):
                co_resolution = float(a.split("=", 1)[1]); i_arg += 1
            elif a == "--exclude-hubs" and i_arg + 1 < len(args):
                co_exclude_hubs = float(args[i_arg + 1]); i_arg += 2
            elif a.startswith("--exclude-hubs="):
                co_exclude_hubs = float(a.split("=", 1)[1]); i_arg += 1
            elif a == "--no-viz" or a.startswith("--min-community-size="):
                i_arg += 1
            elif a.startswith("--"):
                i_arg += 1
            elif watch_path is None:
                watch_path = Path(a); i_arg += 1
            else:
                i_arg += 1
        if watch_path is None:
            watch_path = Path(".")
        graph_json = graph_override if graph_override is not None else watch_path / "graphify-out" / "graph.json"
        if not graph_json.exists():
            print(
                f"error: no graph found at {graph_json} — run /graphify first",
                file=sys.stderr,
            )
            sys.exit(1)
        from networkx.readwrite import json_graph as _jg
        from graphify.build import build_from_json
        from graphify.cluster import cluster, score_all, remap_communities_to_previous
        from graphify.analyze import (
            god_nodes,
            surprising_connections,
            suggest_questions,
        )
        from graphify.report import generate
        from graphify.export import to_json, to_html

        print("Loading existing graph...")
        _enforce_graph_size_cap_or_exit(graph_json)
        _raw = json.loads(graph_json.read_text(encoding="utf-8"))
        _directed = bool(_raw.get("directed", False))
        G = build_from_json(_raw, directed=_directed)
        print(f"Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges")
        print("Re-clustering...")
        communities = cluster(G, resolution=co_resolution, exclude_hubs_percentile=co_exclude_hubs)
        # Mirror the watch/update path (#822): map new cids to prior ones by
        # node-overlap so the existing .graphify_labels.json keeps attaching
        # to the same conceptual community after re-clustering. Without this,
        # labels follow raw cid index and become misaligned whenever the
        # graph has changed between labeling and cluster-only (#1027).
        previous_node_community = {
            n["id"]: n["community"]
            for n in _raw.get("nodes", [])
            if n.get("community") is not None and n.get("id") is not None
        }
        if previous_node_community:
            communities = remap_communities_to_previous(communities, previous_node_community)
        cohesion = score_all(G, communities)
        gods = god_nodes(G)
        surprises = surprising_connections(G, communities)
        out = watch_path / "graphify-out"
        out.mkdir(parents=True, exist_ok=True)
        labels_path = out / ".graphify_labels.json"
        if labels_path.exists() and not force_relabel:
            try:
                labels = {int(k): v for k, v in json.loads(labels_path.read_text(encoding="utf-8")).items()}
            except Exception:
                labels = {cid: f"Community {cid}" for cid in communities}
        elif no_label and not force_relabel:
            labels = {cid: f"Community {cid}" for cid in communities}
        else:
            # No labels file yet (or `graphify label` forced a refresh). When run
            # standalone there is no orchestrating agent to do skill.md Step 5, so
            # auto-name communities with the configured backend rather than leave
            # "Community N" (#1097). Degrades to placeholders if no backend/on error.
            from graphify.llm import generate_community_labels
            print("Labeling communities...")
            # The final labels (LLM or placeholder fallback) are persisted to
            # .graphify_labels.json by the unconditional write below.
            labels, _ = generate_community_labels(
                G, communities, backend=label_backend, gods=gods
            )
        questions = suggest_questions(G, communities, labels)
        tokens = {"input": 0, "output": 0}
        from graphify.export import _git_head as _gh
        _commit = _gh()
        report = generate(G, communities, cohesion, labels, gods, surprises,
                          {"warning": "cluster-only mode — file stats not available"},
                          tokens, str(watch_path), suggested_questions=questions,
                          min_community_size=min_community_size, built_at_commit=_commit)
        (out / "GRAPH_REPORT.md").write_text(report, encoding="utf-8")
        from graphify.export import backup_if_protected as _backup
        _backup(out)
        to_json(G, communities, str(out / "graph.json"))
        labels_path.write_text(json.dumps({str(k): v for k, v in labels.items()}, ensure_ascii=False), encoding="utf-8")

        # Mirror watch.py pattern: gate to_html so core outputs (graph.json +
        # GRAPH_REPORT.md) always land. Honor --no-viz explicitly; otherwise
        # fall back to ValueError handling so an oversized graph doesn't crash
        # the CLI mid-write and leave a stale graph.html on disk.
        html_target = out / "graph.html"
        if no_viz:
            if html_target.exists():
                html_target.unlink()
            print(f"Done - {len(communities)} communities. GRAPH_REPORT.md and graph.json updated (--no-viz; graph.html removed).")
        else:
            try:
                to_html(G, communities, str(html_target), community_labels=labels or None)
                print(f"Done - {len(communities)} communities. GRAPH_REPORT.md, graph.json and graph.html updated.")
            except ValueError as viz_err:
                if html_target.exists():
                    html_target.unlink()
                print(f"Skipped graph.html: {viz_err}")
                print(f"Done - {len(communities)} communities. GRAPH_REPORT.md and graph.json updated.")

    elif cmd == "update":
        force = os.environ.get("GRAPHIFY_FORCE", "").lower() in ("1", "true", "yes")
        no_cluster = False
        args = sys.argv[2:]
        watch_arg: str | None = None
        for a in args:
            if a == "--force":
                force = True
                continue
            if a == "--no-cluster":
                no_cluster = True
                continue
            if a.startswith("-"):
                print(f"error: unknown update option: {a}", file=sys.stderr)
                sys.exit(2)
            if watch_arg is not None:
                print("error: update accepts at most one path argument", file=sys.stderr)
                sys.exit(2)
            watch_arg = a

        if watch_arg is not None:
            watch_path = Path(watch_arg)
        else:
            # Try to recover the scan root saved by the last full build
            saved = Path(_GRAPHIFY_OUT) / ".graphify_root"
            if saved.exists():
                watch_path = Path(saved.read_text(encoding="utf-8").strip())
            else:
                watch_path = Path(".")
        if not watch_path.exists():
            print(f"error: path not found: {watch_path}", file=sys.stderr)
            sys.exit(1)
        from graphify.watch import _rebuild_code

        print(f"Re-extracting code files in {watch_path} (no LLM needed)...")
        # Interactive CLI: block on the per-repo lock rather than skip, so the
        # user sees their explicit `graphify update` complete instead of
        # exiting silently when a hook-driven rebuild happens to be running.
        ok = _rebuild_code(watch_path, force=force, no_cluster=no_cluster, block_on_lock=True)
        if ok:
            print("Code graph updated. For doc/paper/image changes run /graphify --update in your AI assistant.")
            if not (
                os.environ.get("GEMINI_API_KEY")
                or os.environ.get("GOOGLE_API_KEY")
                or os.environ.get("MOONSHOT_API_KEY")
                or os.environ.get("DEEPSEEK_API_KEY")
                or os.environ.get("GRAPHIFY_NO_TIPS")
            ):
                print("Tip: set GEMINI_API_KEY or GOOGLE_API_KEY to use Gemini for semantic extraction.")
        else:
            print(
                "Nothing to update or rebuild failed — check output above.",
                file=sys.stderr,
            )
            sys.exit(1)

    elif cmd == "hook-check":
        # Codex Desktop rejects hookSpecificOutput.additionalContext on PreToolUse.
        # Keep this as a cross-platform no-op so installed hooks never break Bash
        # tool calls. Graph guidance reaches the agent via AGENTS.md / skill instead.
        sys.exit(0)
    elif cmd == "check-update":
        if len(sys.argv) < 3:
            print("Usage: graphify check-update <path>", file=sys.stderr)
            sys.exit(1)
        from graphify.watch import check_update

        check_update(Path(sys.argv[2]).resolve())
        sys.exit(0)
    elif cmd == "tree":
        # Emit a D3 v7 collapsible-tree HTML view of graph.json:
        # expand-all / collapse-all / reset-view buttons, multi-line
        # wrapText labels with separately-coloured name + count,
        # depth-based palette, click-to-toggle subtree, hover inspector
        # showing top-K outbound edges per symbol.
        from typing import Optional as _Opt
        from graphify.tree_html import write_tree_html, DEFAULT_MAX_CHILDREN
        graph_path = Path(_GRAPHIFY_OUT) / "graph.json"
        output_path: "_Opt[Path]" = None
        root: "_Opt[str]" = None
        max_children = DEFAULT_MAX_CHILDREN
        top_k_edges = 0
        project_label: "_Opt[str]" = None
        args = sys.argv[2:]
        i_arg = 0
        while i_arg < len(args):
            a = args[i_arg]
            if a == "--graph" and i_arg + 1 < len(args):
                graph_path = Path(args[i_arg + 1]); i_arg += 2
            elif a == "--output" and i_arg + 1 < len(args):
                output_path = Path(args[i_arg + 1]); i_arg += 2
            elif a == "--root" and i_arg + 1 < len(args):
                root = args[i_arg + 1]; i_arg += 2
            elif a == "--max-children" and i_arg + 1 < len(args):
                max_children = int(args[i_arg + 1]); i_arg += 2
            elif a == "--top-k-edges" and i_arg + 1 < len(args):
                top_k_edges = int(args[i_arg + 1]); i_arg += 2
            elif a == "--label" and i_arg + 1 < len(args):
                project_label = args[i_arg + 1]; i_arg += 2
            elif a in ("-h", "--help"):
                print("Usage: graphify tree [--graph PATH] [--output HTML]")
                print("  --graph PATH         path to graph.json (default graphify-out/graph.json)")
                print("  --output HTML        output path (default graphify-out/GRAPH_TREE.html)")
                print("  --root PATH          filesystem root (default: longest common dir of all source_files)")
                print("  --max-children N     cap visible children per node (default 200)")
                print("  --top-k-edges N      pre-compute top-K outbound edges per symbol (default 12)")
                print("  --label NAME         project label shown in the page header")
                return
            else:
                i_arg += 1
        if not graph_path.is_file():
            print(f"error: graph.json not found at {graph_path}", file=sys.stderr)
            sys.exit(1)
        _enforce_graph_size_cap_or_exit(graph_path)
        if output_path is None:
            output_path = graph_path.parent / "GRAPH_TREE.html"
        out = write_tree_html(
            graph_path=graph_path, output_path=output_path,
            root=root, max_children=max_children,
            top_k_edges=top_k_edges, project_label=project_label,
        )
        size_kb = out.stat().st_size / 1024
        print(f"wrote {out} ({size_kb:.1f} KB)")
        print(f"open with: xdg-open {out}  (or file://{out.resolve()})")
        sys.exit(0)

    elif cmd == "merge-driver":
        # git merge driver for graph.json — takes (base, current, other) and writes
        # the union of current+other nodes/edges back to current. Exits 1 on
        # corrupt input so git surfaces the conflict instead of silently
        # accepting a poisoned merge (see F-005).
        # Usage: graphify merge-driver %O %A %B  (set in .git/config merge driver)
        if len(sys.argv) < 5:
            print("Usage: graphify merge-driver <base> <current> <other>", file=sys.stderr)
            sys.exit(1)
        _base_path, _current_path, _other_path = sys.argv[2], sys.argv[3], sys.argv[4]
        # Hard caps so a malicious or corrupted graph.json cannot exhaust memory
        # at parse time. 50 MB / 100k nodes are well above any realistic graph
        # (typical graphs are <5 MB / <50k nodes); anything larger should fail
        # the merge so a human can investigate.
        _MERGE_MAX_BYTES = 50 * 1024 * 1024
        _MERGE_MAX_NODES = 100_000
        import networkx as _nx
        from networkx.readwrite import json_graph as _jg
        def _load_graph(p: str):
            path_obj = Path(p)
            try:
                size = path_obj.stat().st_size
            except OSError as exc:
                raise RuntimeError(f"cannot stat {p}: {exc}") from exc
            if size > _MERGE_MAX_BYTES:
                raise RuntimeError(
                    f"graph.json {p} is {size} bytes, exceeds {_MERGE_MAX_BYTES}-byte cap"
                )
            data = json.loads(path_obj.read_text(encoding="utf-8"))
            try:
                return _jg.node_link_graph(data, edges="links"), data
            except TypeError:
                return _jg.node_link_graph(data), data
        try:
            G_cur, _ = _load_graph(_current_path)
            G_oth, _ = _load_graph(_other_path)
        except Exception as exc:
            print(f"[graphify merge-driver] error loading graphs: {exc}", file=sys.stderr)
            sys.exit(1)  # surface the conflict so git doesn't accept a corrupt merge
        merged = _nx.compose(G_cur, G_oth)
        if merged.number_of_nodes() > _MERGE_MAX_NODES:
            print(
                f"[graphify merge-driver] merged graph has {merged.number_of_nodes()} nodes, "
                f"exceeds {_MERGE_MAX_NODES}-node cap; aborting merge.",
                file=sys.stderr,
            )
            sys.exit(1)
        try:
            out_data = _jg.node_link_data(merged, edges="links")
        except TypeError:
            out_data = _jg.node_link_data(merged)
        Path(_current_path).write_text(json.dumps(out_data, indent=2), encoding="utf-8")
        sys.exit(0)

    elif cmd == "merge-graphs":
        # graphify merge-graphs graph1.json graph2.json ... --out merged.json
        args = sys.argv[2:]
        graph_paths: list[Path] = []
        out_path = Path(_GRAPHIFY_OUT) / "merged-graph.json"
        i = 0
        while i < len(args):
            if args[i] == "--out" and i + 1 < len(args):
                out_path = Path(args[i + 1])
                i += 2
            else:
                graph_paths.append(Path(args[i]))
                i += 1
        if len(graph_paths) < 2:
            print(
                "Usage: graphify merge-graphs <graph1.json> <graph2.json> [...] [--out merged.json]",
                file=sys.stderr,
            )
            sys.exit(1)
        import networkx as _nx
        from networkx.readwrite import json_graph as _jg
        from graphify.build import prefix_graph_for_global as _prefix
        graphs = []
        for gp in graph_paths:
            if not gp.exists():
                print(f"error: not found: {gp}", file=sys.stderr)
                sys.exit(1)
            _enforce_graph_size_cap_or_exit(gp)
            data = json.loads(gp.read_text(encoding="utf-8"))
            # Normalize edges/links key before loading — graphify writes "links"
            # via node_link_data but older runs may have used "edges" (#738).
            if "links" not in data and "edges" in data:
                data = dict(data, links=data["edges"])
            try:
                G = _jg.node_link_graph(data, edges="links")
            except TypeError:
                G = _jg.node_link_graph(data)
            graphs.append(G)
        merged = _nx.Graph()
        for G, gp in zip(graphs, graph_paths):
            repo_tag = gp.parent.parent.name  # graphify-out/../ → repo dir name
            prefixed = _prefix(G, repo_tag)
            merged = _nx.compose(merged, prefixed)
        try:
            out_data = _jg.node_link_data(merged, edges="links")
        except TypeError:
            out_data = _jg.node_link_data(merged)
        out_path.parent.mkdir(parents=True, exist_ok=True)
        out_path.write_text(json.dumps(out_data, indent=2), encoding="utf-8")
        print(f"Merged {len(graphs)} graphs -> {merged.number_of_nodes()} nodes, {merged.number_of_edges()} edges")
        print(f"Written to: {out_path}")

    elif cmd == "clone":
        if len(sys.argv) < 3:
            print(
                "Usage: graphify clone <github-url> [--branch <branch>] [--out <dir>]",
                file=sys.stderr,
            )
            sys.exit(1)
        url = sys.argv[2]
        branch: str | None = None
        out_dir: Path | None = None
        args = sys.argv[3:]
        i = 0
        while i < len(args):
            if args[i] == "--branch" and i + 1 < len(args):
                branch = args[i + 1]
                i += 2
            elif args[i] == "--out" and i + 1 < len(args):
                out_dir = Path(args[i + 1])
                i += 2
            else:
                i += 1
        local_path = _clone_repo(url, branch=branch, out_dir=out_dir)
        print(local_path)

    elif cmd == "export":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd not in ("html", "callflow-html", "obsidian", "wiki", "svg", "graphml", "neo4j"):
            print("Usage: graphify export <format>", file=sys.stderr)
            print("  html      [--graph PATH] [--labels PATH] [--node-limit N] [--no-viz]", file=sys.stderr)
            print("  callflow-html [GRAPH|DIR] [--graph PATH] [--labels PATH] [--report PATH] [--sections PATH] [--output HTML]", file=sys.stderr)
            print("            [--lang auto|zh-CN|en] [--max-sections N] [--diagram-scale N]", file=sys.stderr)
            print("  obsidian  [--graph PATH] [--labels PATH] [--dir PATH]", file=sys.stderr)
            print("  wiki      [--graph PATH] [--labels PATH]", file=sys.stderr)
            print("  svg       [--graph PATH] [--labels PATH]", file=sys.stderr)
            print("  graphml   [--graph PATH]", file=sys.stderr)
            print("  neo4j     [--graph PATH] [--push URI] [--user U] [--password P]", file=sys.stderr)
            print("            (or set NEO4J_PASSWORD instead of --password to keep it off argv)", file=sys.stderr)
            sys.exit(1)

        # Parse shared args
        args = sys.argv[3:]
        graph_path = Path(_GRAPHIFY_OUT) / "graph.json"
        graph_path_explicit = False
        labels_path = Path(_GRAPHIFY_OUT) / ".graphify_labels.json"
        labels_path_explicit = False
        report_path = Path(_GRAPHIFY_OUT) / "GRAPH_REPORT.md"
        report_path_explicit = False
        sections_path: Path | None = None
        callflow_output: Path | None = None
        callflow_lang = "auto"
        callflow_max_sections = 15
        callflow_diagram_scale = 1.0
        callflow_max_diagram_nodes = 18
        callflow_max_diagram_edges = 24
        analysis_path = Path(_GRAPHIFY_OUT) / ".graphify_analysis.json"
        node_limit = 5000
        no_viz = False
        obsidian_dir = Path(_GRAPHIFY_OUT) / "obsidian"
        neo4j_uri: str | None = None
        neo4j_user = "neo4j"
        # F-031: prefer the NEO4J_PASSWORD env var so the password never
        # appears on argv (visible in `ps` output / shell history). The
        # explicit --password flag still overrides it for compatibility.
        neo4j_password: str | None = os.environ.get("NEO4J_PASSWORD") or None
        i = 0
        while i < len(args):
            a = args[i]
            if a == "--graph" and i + 1 < len(args):
                graph_path = Path(args[i + 1])
                graph_path_explicit = True
                i += 2
            elif a == "--labels" and i + 1 < len(args):
                labels_path = Path(args[i + 1])
                labels_path_explicit = True
                i += 2
            elif a == "--report" and i + 1 < len(args):
                report_path = Path(args[i + 1])
                report_path_explicit = True
                i += 2
            elif a == "--sections" and i + 1 < len(args):
                sections_path = Path(args[i + 1]); i += 2
            elif a == "--output" and i + 1 < len(args):
                callflow_output = Path(args[i + 1]).expanduser()
                if not callflow_output.is_absolute():
                    callflow_output = Path.cwd() / callflow_output
                i += 2
            elif a == "--lang" and i + 1 < len(args):
                callflow_lang = args[i + 1]; i += 2
            elif a == "--max-sections" and i + 1 < len(args):
                callflow_max_sections = int(args[i + 1]); i += 2
            elif a == "--diagram-scale" and i + 1 < len(args):
                callflow_diagram_scale = float(args[i + 1]); i += 2
            elif a == "--max-diagram-nodes" and i + 1 < len(args):
                callflow_max_diagram_nodes = int(args[i + 1]); i += 2
            elif a == "--max-diagram-edges" and i + 1 < len(args):
                callflow_max_diagram_edges = int(args[i + 1]); i += 2
            elif a in ("-h", "--help") and subcmd == "callflow-html":
                print("Usage: graphify export callflow-html [GRAPH|DIR] [--graph PATH] [--labels PATH]")
                print("  --report PATH          path to GRAPH_REPORT.md")
                print("  --sections PATH        JSON section definitions")
                print("  --output HTML          output path (default graphify-out/<project>-callflow.html)")
                print("  --lang LANG            auto, zh-CN, en, etc. (default auto)")
                print("  --max-sections N       maximum auto-derived sections (default 15)")
                print("  --diagram-scale N      Mermaid diagram scale (default 1.0)")
                print("  --max-diagram-nodes N  representative nodes per section (default 18)")
                print("  --max-diagram-edges N  representative edges per section (default 24)")
                sys.exit(0)
            elif a == "--node-limit" and i + 1 < len(args):
                node_limit = int(args[i + 1]); i += 2
            elif a == "--no-viz":
                no_viz = True; i += 1
            elif a == "--dir" and i + 1 < len(args):
                obsidian_dir = Path(args[i + 1]); i += 2
            elif a == "--push" and i + 1 < len(args):
                neo4j_uri = args[i + 1]; i += 2
            elif a == "--user" and i + 1 < len(args):
                neo4j_user = args[i + 1]; i += 2
            elif a == "--password" and i + 1 < len(args):
                neo4j_password = args[i + 1]; i += 2
            elif subcmd == "callflow-html" and not a.startswith("-") and not graph_path_explicit:
                candidate = Path(a)
                if candidate.name == "graph.json" or candidate.suffix.lower() == ".json":
                    graph_path = candidate
                elif (candidate / "graph.json").exists():
                    graph_path = candidate / "graph.json"
                else:
                    graph_path = candidate / _GRAPHIFY_OUT / "graph.json"
                graph_path_explicit = True
                i += 1
            else:
                i += 1

        graph_path = graph_path.expanduser()
        if graph_path_explicit:
            graph_out_dir = graph_path.parent
            if not labels_path_explicit:
                labels_path = graph_out_dir / ".graphify_labels.json"
            if not report_path_explicit:
                report_path = graph_out_dir / "GRAPH_REPORT.md"
        labels_path = labels_path.expanduser()
        report_path = report_path.expanduser()

        if not graph_path.exists():
            print(f"error: graph not found: {graph_path}. Run /graphify <path> first.", file=sys.stderr)
            sys.exit(1)

        if subcmd == "callflow-html":
            from graphify.callflow_html import write_callflow_html as _write_callflow_html
            out = _write_callflow_html(
                graph=graph_path,
                report=report_path,
                labels=labels_path,
                sections=sections_path,
                output=callflow_output,
                lang=callflow_lang,
                max_sections=callflow_max_sections,
                diagram_scale=callflow_diagram_scale,
                max_diagram_nodes=callflow_max_diagram_nodes,
                max_diagram_edges=callflow_max_diagram_edges,
                verbose=True,
            )
            print(f"callflow HTML written - open in any browser: {out}")
            sys.exit(0)

        from networkx.readwrite import json_graph as _jg
        from graphify.build import build_from_json as _bfj

        _enforce_graph_size_cap_or_exit(graph_path)
        _raw = json.loads(graph_path.read_text(encoding="utf-8"))
        if "links" not in _raw and "edges" in _raw:
            _raw = dict(_raw, links=_raw["edges"])
        try:
            G = _jg.node_link_graph(_raw, edges="links")
        except TypeError:
            G = _jg.node_link_graph(_raw)

        # Load optional analysis/labels
        communities: dict[int, list[str]] = {}
        if analysis_path.exists():
            _an = json.loads(analysis_path.read_text(encoding="utf-8"))
            communities = {int(k): v for k, v in _an.get("communities", {}).items()}
            cohesion: dict[int, float] = {int(k): v for k, v in _an.get("cohesion", {}).items()}
            gods_data = _an.get("gods", [])
        else:
            cohesion = {}
            gods_data = []

        # Fallback: graph.json carries the per-node community as a node attribute
        # (`to_json` writes it on every node). The analysis sidecar is the
        # canonical source — but the post-commit / watch rebuild path doesn't
        # regenerate it, and `extract` may have its temp files cleaned up. When
        # that happens, `graphify export html` previously bailed with
        # "Single community - aggregated view not useful." even though the
        # per-node attribute had the right data all along. Reconstruct from
        # the graph itself so downstream subcommands (html, obsidian, wiki,
        # svg, graphml, neo4j) don't silently produce a degraded artifact.
        if not communities:
            reconstructed: dict[int, list[str]] = {}
            for node_id, data in G.nodes(data=True):
                cid_raw = data.get("community")
                if cid_raw is None:
                    continue
                try:
                    cid = int(cid_raw)
                except (TypeError, ValueError):
                    continue
                reconstructed.setdefault(cid, []).append(str(node_id))
            if reconstructed:
                communities = reconstructed

        labels: dict[int, str] = {}
        if labels_path.exists():
            labels = {int(k): v for k, v in json.loads(labels_path.read_text(encoding="utf-8")).items()}

        out_dir = graph_path.parent

        if subcmd == "html":
            from graphify.export import to_html as _to_html
            if no_viz:
                html_target = out_dir / "graph.html"
                if html_target.exists():
                    html_target.unlink()
                print("--no-viz: skipped graph.html")
            else:
                _to_html(G, communities, str(out_dir / "graph.html"),
                         community_labels=labels or None, node_limit=node_limit)
                if G.number_of_nodes() <= node_limit:
                    print(f"graph.html written - open in any browser, no server needed")

        elif subcmd == "obsidian":
            from graphify.export import to_obsidian as _to_obsidian, to_canvas as _to_canvas
            n = _to_obsidian(G, communities, str(obsidian_dir),
                             community_labels=labels or None, cohesion=cohesion or None)
            print(f"Obsidian vault: {n} notes in {obsidian_dir}/")
            _to_canvas(G, communities, str(obsidian_dir / "graph.canvas"),
                       community_labels=labels or None)
            print(f"Canvas: {obsidian_dir}/graph.canvas")
            print(f"Open {obsidian_dir}/ as a vault in Obsidian.")

        elif subcmd == "wiki":
            from graphify.wiki import to_wiki as _to_wiki
            from graphify.analyze import god_nodes as _god_nodes
            if not communities:
                print(
                    "error: .graphify_analysis.json is missing or empty — refusing to export wiki to prevent data loss.\n"
                    "Run `graphify extract .` (or `graphify cluster-only .`) to regenerate community data first.",
                    file=sys.stderr,
                )
                sys.exit(1)
            if not gods_data:
                gods_data = _god_nodes(G)
            n = _to_wiki(G, communities, str(out_dir / "wiki"),
                         community_labels=labels or None, cohesion=cohesion or None,
                         god_nodes_data=gods_data)
            print(f"Wiki: {n} articles written to {out_dir}/wiki/")
            print(f"  {out_dir}/wiki/index.md  ->  agent entry point")

        elif subcmd == "svg":
            from graphify.export import to_svg as _to_svg
            _to_svg(G, communities, str(out_dir / "graph.svg"),
                    community_labels=labels or None)
            print(f"graph.svg written - embeds in Obsidian, Notion, GitHub READMEs")

        elif subcmd == "graphml":
            from graphify.export import to_graphml as _to_graphml
            _to_graphml(G, communities, str(out_dir / "graph.graphml"))
            print(f"graph.graphml written - open in Gephi, yEd, or any GraphML tool")

        elif subcmd == "neo4j":
            if neo4j_uri:
                from graphify.export import push_to_neo4j as _push
                if neo4j_password is None:
                    print("error: --password required for --push", file=sys.stderr)
                    sys.exit(1)
                result = _push(G, uri=neo4j_uri, user=neo4j_user,
                               password=neo4j_password, communities=communities)
                print(f"Pushed to Neo4j: {result['nodes']} nodes, {result['edges']} edges")
            else:
                from graphify.export import to_cypher as _to_cypher
                _to_cypher(G, str(out_dir / "cypher.txt"))
                print(f"cypher.txt written - import with: cypher-shell < {out_dir}/cypher.txt")

    elif cmd == "benchmark":
        from graphify.benchmark import run_benchmark, print_benchmark

        graph_path = sys.argv[2] if len(sys.argv) > 2 else "graphify-out/graph.json"
        _enforce_graph_size_cap_or_exit(Path(graph_path))
        # Try to load corpus_words from detect output
        corpus_words = None
        detect_path = Path(".graphify_detect.json")
        if detect_path.exists():
            try:
                detect_data = json.loads(detect_path.read_text(encoding="utf-8"))
                corpus_words = detect_data.get("total_words")
            except Exception:
                pass
        result = run_benchmark(graph_path, corpus_words=corpus_words)
        print_benchmark(result)

    elif cmd == "global":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        from graphify.global_graph import (
            global_add as _global_add,
            global_remove as _global_remove,
            global_list as _global_list,
            global_path as _global_path,
        )
        if subcmd == "add":
            # graphify global add <graph.json> [--as <tag>]
            args = sys.argv[3:]
            source = None
            tag = None
            i = 0
            while i < len(args):
                if args[i] == "--as" and i + 1 < len(args):
                    tag = args[i + 1]; i += 2
                elif not source:
                    source = Path(args[i]); i += 1
                else:
                    i += 1
            if not source:
                print("Usage: graphify global add <graph.json> [--as <repo-tag>]", file=sys.stderr)
                sys.exit(1)
            tag = tag or source.parent.parent.name
            try:
                result = _global_add(source, tag)
                if result["skipped"]:
                    print(f"'{tag}' unchanged since last add - global graph not modified.")
                else:
                    print(f"Added '{tag}' to global graph: +{result['nodes_added']} nodes, "
                          f"-{result['nodes_removed']} pruned. Global: {_global_path()}")
            except Exception as exc:
                print(f"error: {exc}", file=sys.stderr); sys.exit(1)
        elif subcmd == "remove":
            tag = sys.argv[3] if len(sys.argv) > 3 else ""
            if not tag:
                print("Usage: graphify global remove <repo-tag>", file=sys.stderr); sys.exit(1)
            try:
                removed = _global_remove(tag)
                print(f"Removed '{tag}' from global graph ({removed} nodes pruned).")
            except KeyError as exc:
                print(f"error: {exc}", file=sys.stderr); sys.exit(1)
        elif subcmd == "list":
            repos = _global_list()
            if not repos:
                print("Global graph is empty. Use 'graphify global add' to add a project.")
            else:
                print(f"Global graph: {_global_path()}")
                for tag, info in repos.items():
                    print(f"  {tag}: {info.get('node_count', '?')} nodes, added {info.get('added_at', '?')[:10]}")
        elif subcmd == "path":
            print(_global_path())
        else:
            print("Usage: graphify global [add|remove|list|path]", file=sys.stderr); sys.exit(1)

    elif cmd == "extract":
        # Headless full-pipeline extraction for CI / scripts (#698).
        # Runs detect -> AST extraction on code -> semantic LLM extraction on
        # docs/papers/images -> merge -> build -> cluster -> write outputs.
        # Unlike the skill.md path (which runs through Claude Code subagents),
        # this calls extract_corpus_parallel directly using whichever backend
        # has an API key set.
        if len(sys.argv) < 3:
            print(
                "Usage: graphify extract <path> [--backend gemini|kimi|claude|openai|deepseek|ollama] "
                "[--model M] [--mode deep] [--out DIR] [--google-workspace] [--no-cluster] "
                "[--max-workers N] [--token-budget N] [--max-concurrency N] "
                "[--api-timeout S] [--postgres DSN]",
                file=sys.stderr,
            )
            sys.exit(1)

        has_path = True
        if sys.argv[2].startswith("-"):
            has_path = False
            target = Path(".").resolve()
        else:
            target = Path(sys.argv[2]).resolve()
            if not target.exists():
                print(f"error: path not found: {target}", file=sys.stderr)
                sys.exit(1)

        backend: str | None = None
        model: str | None = None
        extract_mode: str | None = None
        out_dir: Path | None = None
        cli_postgres_dsn: str | None = None
        no_cluster = False
        dedup_llm = False
        google_workspace = False
        global_merge = False
        global_repo_tag: str | None = None
        # Performance/tuning knobs (issue #792). None means "use library default".
        cli_max_workers: int | None = None
        cli_token_budget: int | None = None
        cli_max_concurrency: int | None = None
        cli_api_timeout: float | None = None
        # Clustering tuning knobs
        cli_resolution: float = 1.0
        cli_exclude_hubs: float | None = None
        cli_excludes: list[str] = []

        def _parse_int(name: str, raw: str) -> int:
            try:
                v = int(raw)
            except ValueError:
                print(f"error: {name} must be a positive integer (got {raw!r})", file=sys.stderr)
                sys.exit(2)
            if v <= 0:
                print(f"error: {name} must be > 0 (got {v})", file=sys.stderr)
                sys.exit(2)
            return v

        def _parse_float(name: str, raw: str) -> float:
            try:
                v = float(raw)
            except ValueError:
                print(f"error: {name} must be a positive number (got {raw!r})", file=sys.stderr)
                sys.exit(2)
            if v <= 0:
                print(f"error: {name} must be > 0 (got {v})", file=sys.stderr)
                sys.exit(2)
            return v

        args = sys.argv[3:] if has_path else sys.argv[2:]
        i = 0
        while i < len(args):
            a = args[i]
            if a == "--backend" and i + 1 < len(args):
                backend = args[i + 1]; i += 2
            elif a.startswith("--backend="):
                backend = a.split("=", 1)[1]; i += 1
            elif a == "--model" and i + 1 < len(args):
                model = args[i + 1]; i += 2
            elif a.startswith("--model="):
                model = a.split("=", 1)[1]; i += 1
            elif a == "--mode" and i + 1 < len(args):
                extract_mode = args[i + 1]; i += 2
            elif a.startswith("--mode="):
                extract_mode = a.split("=", 1)[1]; i += 1
            elif a == "--out" and i + 1 < len(args):
                out_dir = Path(args[i + 1]); i += 2
            elif a.startswith("--out="):
                out_dir = Path(a.split("=", 1)[1]); i += 1
            elif a == "--no-cluster":
                no_cluster = True; i += 1
            elif a == "--dedup-llm":
                dedup_llm = True; i += 1
            elif a == "--google-workspace":
                google_workspace = True; i += 1
            elif a == "--global":
                global_merge = True; i += 1
            elif a == "--as" and i + 1 < len(args):
                global_repo_tag = args[i + 1]; i += 2
            elif a == "--max-workers" and i + 1 < len(args):
                cli_max_workers = _parse_int("--max-workers", args[i + 1]); i += 2
            elif a.startswith("--max-workers="):
                cli_max_workers = _parse_int("--max-workers", a.split("=", 1)[1]); i += 1
            elif a == "--token-budget" and i + 1 < len(args):
                cli_token_budget = _parse_int("--token-budget", args[i + 1]); i += 2
            elif a.startswith("--token-budget="):
                cli_token_budget = _parse_int("--token-budget", a.split("=", 1)[1]); i += 1
            elif a == "--max-concurrency" and i + 1 < len(args):
                cli_max_concurrency = _parse_int("--max-concurrency", args[i + 1]); i += 2
            elif a.startswith("--max-concurrency="):
                cli_max_concurrency = _parse_int("--max-concurrency", a.split("=", 1)[1]); i += 1
            elif a == "--api-timeout" and i + 1 < len(args):
                cli_api_timeout = _parse_float("--api-timeout", args[i + 1]); i += 2
            elif a.startswith("--api-timeout="):
                cli_api_timeout = _parse_float("--api-timeout", a.split("=", 1)[1]); i += 1
            elif a == "--resolution" and i + 1 < len(args):
                cli_resolution = _parse_float("--resolution", args[i + 1]); i += 2
            elif a.startswith("--resolution="):
                cli_resolution = _parse_float("--resolution", a.split("=", 1)[1]); i += 1
            elif a == "--exclude-hubs" and i + 1 < len(args):
                cli_exclude_hubs = float(args[i + 1]); i += 2
            elif a.startswith("--exclude-hubs="):
                cli_exclude_hubs = float(a.split("=", 1)[1]); i += 1
            elif a == "--exclude" and i + 1 < len(args):
                cli_excludes.append(args[i + 1]); i += 2
            elif a.startswith("--exclude="):
                cli_excludes.append(a.split("=", 1)[1]); i += 1
            elif a == "--postgres" and i + 1 < len(args):
                cli_postgres_dsn = args[i + 1]; i += 2
            elif a.startswith("--postgres="):
                cli_postgres_dsn = a.split("=", 1)[1]; i += 1
            else:
                i += 1

        if not has_path and cli_postgres_dsn is None:
            print("error: must specify a path to scan or a --postgres DSN", file=sys.stderr)
            sys.exit(1)

        _VALID_MODES = {"deep"}
        if extract_mode is not None and extract_mode not in _VALID_MODES:
            print(
                f"error: unknown --mode '{extract_mode}'. "
                f"Available: {', '.join(sorted(_VALID_MODES))}",
                file=sys.stderr,
            )
            sys.exit(2)
        deep_mode = extract_mode == "deep"
        if deep_mode:
            print("[graphify extract] deep mode enabled: richer semantic extraction")

        # CLI flag wins over env var. Setting GRAPHIFY_API_TIMEOUT here so
        # _call_openai_compat picks it up without needing a new kwarg path.
        if cli_api_timeout is not None:
            os.environ["GRAPHIFY_API_TIMEOUT"] = str(cli_api_timeout)
        if cli_max_workers is not None:
            os.environ["GRAPHIFY_MAX_WORKERS"] = str(cli_max_workers)

        # Resolve output dir. The user-facing contract is "<out>/graphify-out/"
        # so a fresh checkout writes graphify-out/ at the project root, matching
        # the skill.md pipeline.
        out_root = (out_dir.resolve() if out_dir else target)
        graphify_out = out_root / "graphify-out"
        graphify_out.mkdir(parents=True, exist_ok=True)

        from graphify.detect import (
            detect as _detect,
            detect_incremental as _detect_incremental,
            save_manifest as _save_manifest,
        )
        manifest_path = graphify_out / "manifest.json"
        existing_graph_path = graphify_out / "graph.json"
        incremental_mode = manifest_path.exists() and existing_graph_path.exists() if has_path else False

        if not has_path:
            code_files = []
            doc_files = []
            paper_files = []
            image_files = []
            deleted_files = []
            unchanged_total = 0
            files_by_type = {}
        elif incremental_mode:
            print(f"[graphify extract] incremental scan of {target}")
            detection = _detect_incremental(
                target,
                manifest_path=str(manifest_path),
                google_workspace=google_workspace or None,
                extra_excludes=cli_excludes or None,
            )
            files_by_type = detection.get("files", {})
            new_by_type = detection.get("new_files", {})
            code_files = [Path(p) for p in new_by_type.get("code", [])]
            doc_files = [Path(p) for p in new_by_type.get("document", [])]
            paper_files = [Path(p) for p in new_by_type.get("paper", [])]
            image_files = [Path(p) for p in new_by_type.get("image", [])]
            deleted_files = list(detection.get("deleted_files", []))
            unchanged_total = sum(len(v) for v in detection.get("unchanged_files", {}).values())
        else:
            print(f"[graphify extract] scanning {target}")
            detection = _detect(target, google_workspace=google_workspace or None, extra_excludes=cli_excludes or None)
            files_by_type = detection.get("files", {})
            code_files = [Path(p) for p in files_by_type.get("code", [])]
            doc_files = [Path(p) for p in files_by_type.get("document", [])]
            paper_files = [Path(p) for p in files_by_type.get("paper", [])]
            image_files = [Path(p) for p in files_by_type.get("image", [])]
            deleted_files = []
            unchanged_total = 0

        semantic_files = doc_files + paper_files + image_files
        if incremental_mode:
            print(
                f"[graphify extract] {len(code_files)} code, {len(doc_files)} docs, "
                f"{len(paper_files)} papers, {len(image_files)} images changed; "
                f"{unchanged_total} unchanged; {len(deleted_files)} deleted"
            )
        else:
            print(
                f"[graphify extract] found {len(code_files)} code, "
                f"{len(doc_files)} docs, {len(paper_files)} papers, "
                f"{len(image_files)} images"
            )

        # Resolve the LLM backend only now that we know whether the corpus
        # needs one. A code-only corpus is pure local AST and must not require
        # an API key; the key is enforced below only when there's LLM work.
        from graphify.llm import (
            BACKENDS as _BACKENDS,
            detect_backend as _detect_backend,
            estimate_cost as _estimate_cost,
            extract_corpus_parallel as _extract_corpus_parallel,
            _format_backend_env_keys,
            _get_backend_api_key,
        )
        needs_llm = bool(semantic_files) or dedup_llm
        if backend is None and needs_llm:
            backend = _detect_backend()
        if backend is not None and backend not in _BACKENDS:
            print(
                f"error: unknown backend '{backend}'. "
                f"Available: {', '.join(sorted(_BACKENDS))}",
                file=sys.stderr,
            )
            sys.exit(1)
        if needs_llm:
            if backend is None:
                reasons = []
                if semantic_files:
                    reasons.append(
                        f"{len(semantic_files)} doc/paper/image file(s) need semantic extraction"
                    )
                if dedup_llm:
                    reasons.append("--dedup-llm was passed")
                print(
                    "error: no LLM API key found (" + "; ".join(reasons) + "). "
                    "Set GEMINI_API_KEY or GOOGLE_API_KEY (gemini), MOONSHOT_API_KEY "
                    "(kimi), ANTHROPIC_API_KEY (claude), OPENAI_API_KEY (openai), "
                    "DEEPSEEK_API_KEY (deepseek), or pass --backend. A code-only "
                    "corpus needs no key.",
                    file=sys.stderr,
                )
                sys.exit(1)
            if backend == "ollama":
                from graphify.llm import _validate_ollama_base_url
                _oll_url = os.environ.get("OLLAMA_BASE_URL", _BACKENDS["ollama"].get("base_url", ""))
                try:
                    _validate_ollama_base_url(_oll_url, warn=False)
                except ValueError as exc:
                    print(f"error: {exc}", file=sys.stderr)
                    sys.exit(2)
            if not _get_backend_api_key(backend):
                allow_no_key = False
                if backend == "ollama":
                    from urllib.parse import urlparse
                    ollama_url = os.environ.get(
                        "OLLAMA_BASE_URL",
                        _BACKENDS["ollama"].get("base_url", ""),
                    )
                    try:
                        host = (urlparse(ollama_url).hostname or "").lower()
                    except Exception:
                        host = ""
                    allow_no_key = (
                        host in ("localhost", "127.0.0.1", "::1")
                        or host.startswith("127.")
                    )
                elif backend == "bedrock":
                    allow_no_key = bool(
                        os.environ.get("AWS_PROFILE")
                        or os.environ.get("AWS_REGION")
                        or os.environ.get("AWS_DEFAULT_REGION")
                        or os.environ.get("AWS_ACCESS_KEY_ID")
                    )
                elif backend == "claude-cli":
                    import shutil as _shutil
                    allow_no_key = _shutil.which("claude") is not None
                    if not allow_no_key:
                        print(
                            "error: backend 'claude-cli' requires the `claude` CLI on $PATH "
                            "(install Claude Code and run `claude` once to authenticate).",
                            file=sys.stderr,
                        )
                        sys.exit(1)
                if not allow_no_key:
                    print(
                        f"error: backend '{backend}' requires {_format_backend_env_keys(backend)} to be set.",
                        file=sys.stderr,
                    )
                    sys.exit(1)

        # AST extraction on code files. Empty code list (docs-only corpus) is
        # the issue #698 case — skip cleanly instead of crashing inside extract().
        ast_result: dict = {"nodes": [], "edges": [], "input_tokens": 0, "output_tokens": 0}
        if code_files:
            from graphify.extract import extract as _ast_extract
            ast_kwargs: dict = {"cache_root": target}
            if cli_max_workers is not None:
                ast_kwargs["max_workers"] = cli_max_workers
            print(f"[graphify extract] AST extraction on {len(code_files)} code files...")
            try:
                ast_result = _ast_extract(code_files, **ast_kwargs)
            except Exception as exc:
                print(f"[graphify extract] AST extraction failed: {exc}", file=sys.stderr)
                ast_result = {"nodes": [], "edges": [], "input_tokens": 0, "output_tokens": 0}

        # Semantic extraction on docs/papers/images. Check cache first.
        from graphify.cache import (
            check_semantic_cache as _check_semantic_cache,
            save_semantic_cache as _save_semantic_cache,
        )
        sem_result: dict = {
            "nodes": [], "edges": [], "hyperedges": [],
            "input_tokens": 0, "output_tokens": 0,
        }
        sem_cache_hits = 0
        sem_cache_misses = 0
        if semantic_files:
            sem_paths_str = [str(p) for p in semantic_files]
            cached_nodes, cached_edges, cached_hyperedges, uncached_paths = (
                _check_semantic_cache(sem_paths_str, root=target)
            )
            sem_cache_hits = len(semantic_files) - len(uncached_paths)
            sem_cache_misses = len(uncached_paths)
            sem_result["nodes"].extend(cached_nodes)
            sem_result["edges"].extend(cached_edges)
            sem_result["hyperedges"].extend(cached_hyperedges)
            if sem_cache_hits:
                print(f"[graphify extract] semantic cache: {sem_cache_hits} hit / {sem_cache_misses} miss")

            if uncached_paths:
                print(f"[graphify extract] semantic extraction on {len(uncached_paths)} files via {backend}...")
                corpus_kwargs: dict = {
                    "backend": backend,
                    "model": model,
                    "root": target,
                }
                if deep_mode:
                    corpus_kwargs["deep_mode"] = True
                if cli_token_budget is not None:
                    corpus_kwargs["token_budget"] = cli_token_budget
                if cli_max_concurrency is not None:
                    corpus_kwargs["max_concurrency"] = cli_max_concurrency

                # Minimal progress callback so the CLI is no longer silent
                # during long local-inference runs (issue #792 addendum).
                # Also track per-chunk success so we can fail loudly when
                # every chunk errors (e.g. missing backend SDK package).
                _chunk_stats = {"total": 0, "succeeded": 0}
                def _progress(idx: int, total: int, _result: dict) -> None:
                    _chunk_stats["total"] = total
                    _chunk_stats["succeeded"] += 1
                    print(
                        f"[graphify extract] chunk {idx + 1}/{total} done",
                        flush=True,
                    )
                corpus_kwargs["on_chunk_done"] = _progress

                try:
                    fresh = _extract_corpus_parallel(
                        [Path(p) for p in uncached_paths],
                        **corpus_kwargs,
                    )
                except ImportError as exc:
                    print(f"error: {exc}", file=sys.stderr)
                    sys.exit(1)
                except Exception as exc:
                    print(
                        f"[graphify extract] semantic extraction failed: {exc}",
                        file=sys.stderr,
                    )
                    fresh = {"nodes": [], "edges": [], "hyperedges": [], "input_tokens": 0, "output_tokens": 0}

                # on_chunk_done only fires after a chunk succeeds. If fresh
                # semantic extraction was requested and no chunks completed,
                # fail instead of writing an AST-only graph with exit 0.
                if uncached_paths and _chunk_stats["succeeded"] == 0:
                    print(
                        f"[graphify extract] error: all semantic chunks failed "
                        f"for backend '{backend}' ({len(uncached_paths)} uncached files) - "
                        f"see per-chunk errors above. If you see 'requires the X package', "
                        f"run `pip install X` and retry.",
                        file=sys.stderr,
                    )
                    sys.exit(1)
                try:
                    _save_semantic_cache(
                        fresh.get("nodes", []),
                        fresh.get("edges", []),
                        fresh.get("hyperedges", []),
                        root=target,
                    )
                except Exception as exc:
                    print(f"[graphify extract] warning: could not write semantic cache: {exc}", file=sys.stderr)
                sem_result["nodes"].extend(fresh.get("nodes", []))
                sem_result["edges"].extend(fresh.get("edges", []))
                sem_result["hyperedges"].extend(fresh.get("hyperedges", []))
                sem_result["input_tokens"] += fresh.get("input_tokens", 0)
                sem_result["output_tokens"] += fresh.get("output_tokens", 0)

        pg_result: dict = {"nodes": [], "edges": []}
        if cli_postgres_dsn is not None:
            from graphify.pg_introspect import introspect_postgres
            print(f"[graphify extract] introspecting PostgreSQL schema...")
            try:
                pg_result = introspect_postgres(cli_postgres_dsn)
            except (ConnectionError, ImportError) as exc:
                print(f"error: {exc}", file=sys.stderr)
                sys.exit(1)
            print(f"[graphify extract] PostgreSQL: {len(pg_result['nodes'])} nodes, "
                  f"{len(pg_result['edges'])} edges")

        # Merge AST + semantic + pg_result. Order matters for deduplication: passing AST
        # first means semantic node attributes win on collision (richer labels
        # for symbols also referenced in docs). Hyperedges only come from the
        # semantic side.
        merged: dict = {
            "nodes": list(ast_result.get("nodes", [])) + list(sem_result.get("nodes", [])) + list(pg_result.get("nodes", [])),
            "edges": list(ast_result.get("edges", [])) + list(sem_result.get("edges", [])) + list(pg_result.get("edges", [])),
            "hyperedges": list(sem_result.get("hyperedges", [])),
            "input_tokens": ast_result.get("input_tokens", 0) + sem_result.get("input_tokens", 0),
            "output_tokens": ast_result.get("output_tokens", 0) + sem_result.get("output_tokens", 0),
        }

        graph_json_path = graphify_out / "graph.json"
        analysis_path = graphify_out / ".graphify_analysis.json"

        # Build a manifest-safe files dict: only stamp semantic_hash for files
        # that actually produced output (cache hit or fresh extraction). Files
        # whose chunk failed have no source_file entry in sem_result — leaving
        # their semantic_hash empty so detect_incremental re-queues them (#933).
        _sem_extracted: set[str] = {
            n.get("source_file", "") for n in sem_result.get("nodes", [])
        } | {
            e.get("source_file", "") for e in sem_result.get("edges", [])
        }
        _sem_extracted.discard("")
        _sem_types = {"document", "paper", "image"}
        _manifest_files = {
            ftype: [f for f in flist if ftype not in _sem_types or f in _sem_extracted]
            for ftype, flist in files_by_type.items()
        }

        if no_cluster:
            # --no-cluster: dump the raw merged extraction as graph.json.
            # No NetworkX, no community detection, no analysis sidecar.
            from graphify.export import backup_if_protected as _backup
            _backup(graphify_out)
            graph_json_path.write_text(
                json.dumps(merged, indent=2), encoding="utf-8"
            )
            cost = _estimate_cost(
                backend, merged["input_tokens"], merged["output_tokens"]
            )
            print(
                f"[graphify extract] wrote {graph_json_path} — "
                f"{len(merged['nodes'])} nodes, {len(merged['edges'])} edges "
                f"(no clustering)"
            )
            if merged["input_tokens"] or merged["output_tokens"]:
                print(
                    f"[graphify extract] tokens: "
                    f"{merged['input_tokens']:,} in / "
                    f"{merged['output_tokens']:,} out, "
                    f"est. cost: ${cost:.4f}"
                )
            try:
                _save_manifest(_manifest_files, manifest_path=str(manifest_path), kind="both", root=target)
            except Exception as exc:
                print(f"[graphify extract] warning: could not write manifest: {exc}", file=sys.stderr)
            if global_merge:
                from graphify.global_graph import global_add as _global_add
                _tag = global_repo_tag or target.name
                try:
                    result = _global_add(graphify_out / "graph.json", _tag)
                    if result["skipped"]:
                        print(f"[graphify global] '{_tag}' unchanged since last add - skipped.")
                    else:
                        print(f"[graphify global] '{_tag}' merged into global graph "
                              f"(+{result['nodes_added']} nodes, -{result['nodes_removed']} pruned).")
                except Exception as exc:
                    print(f"[graphify global] warning: failed to merge into global graph: {exc}", file=sys.stderr)
            sys.exit(0)

        # Build graph + cluster + score + write.
        from graphify.build import (
            build as _build,
            build_from_json as _build_from_json,
            build_merge as _build_merge,
        )
        from graphify.cluster import cluster as _cluster, score_all as _score_all
        from graphify.export import to_json as _to_json
        from graphify.analyze import god_nodes as _god_nodes, surprising_connections as _surprising
        dedup_backend = backend if dedup_llm else None
        if incremental_mode:
            G = _build_merge(
                [merged],
                graph_path=existing_graph_path,
                prune_sources=deleted_files or None,
                dedup=True,
                dedup_llm_backend=dedup_backend,
                root=target,
            )
        else:
            G = _build([merged], dedup=True, dedup_llm_backend=dedup_backend, root=target)
        if G.number_of_nodes() == 0:
            print(
                "[graphify extract] graph is empty — extraction produced no nodes. "
                "Possible causes: all files skipped, binary-only corpus, or LLM "
                "returned no edges.",
                file=sys.stderr,
            )
            sys.exit(1)

        communities = _cluster(G, resolution=cli_resolution, exclude_hubs_percentile=cli_exclude_hubs)
        cohesion = _score_all(G, communities)
        try:
            gods = _god_nodes(G)
        except Exception:
            gods = []
        try:
            surprises = _surprising(G, communities)
        except Exception:
            surprises = []

        from graphify.export import backup_if_protected as _backup
        _backup(graphify_out)
        _to_json(G, communities, str(graph_json_path), force=True)
        if merged.get("output_tokens", 0) > 0:
            (graphify_out / ".graphify_semantic_marker").write_text(
                json.dumps({"output_tokens": merged["output_tokens"]}), encoding="utf-8"
            )
        if global_merge:
            from graphify.global_graph import global_add as _global_add
            _tag = global_repo_tag or target.name
            try:
                result = _global_add(graphify_out / "graph.json", _tag)
                if result["skipped"]:
                    print(f"[graphify global] '{_tag}' unchanged since last add - skipped.")
                else:
                    print(f"[graphify global] '{_tag}' merged into global graph "
                          f"(+{result['nodes_added']} nodes, -{result['nodes_removed']} pruned).")
            except Exception as exc:
                print(f"[graphify global] warning: failed to merge into global graph: {exc}", file=sys.stderr)
        analysis = {
            "communities": {str(k): v for k, v in communities.items()},
            "cohesion": {str(k): v for k, v in cohesion.items()},
            "gods": gods,
            "surprises": surprises,
            "tokens": {
                "input": merged["input_tokens"],
                "output": merged["output_tokens"],
            },
        }
        analysis_path.write_text(json.dumps(analysis, indent=2), encoding="utf-8")
        try:
            _save_manifest(_manifest_files, manifest_path=str(manifest_path), kind="both", root=target)
        except Exception as exc:
            print(f"[graphify extract] warning: could not write manifest: {exc}", file=sys.stderr)

        cost = _estimate_cost(backend, merged["input_tokens"], merged["output_tokens"])
        print(
            f"[graphify extract] wrote {graph_json_path}: "
            f"{G.number_of_nodes()} nodes, {G.number_of_edges()} edges, "
            f"{len(communities)} communities"
        )
        print(f"[graphify extract] wrote {analysis_path}")
        if incremental_mode:
            print(
                f"[graphify extract] incremental summary: "
                f"{sem_cache_hits + unchanged_total} files cached/unchanged, "
                f"{len(code_files) + sem_cache_misses} re-extracted, "
                f"{len(deleted_files)} deleted"
            )
        elif sem_cache_hits:
            print(f"[graphify extract] semantic cache: {sem_cache_hits} cached, {sem_cache_misses} re-extracted")
        if merged["input_tokens"] or merged["output_tokens"]:
            print(
                f"[graphify extract] tokens: "
                f"{merged['input_tokens']:,} in / "
                f"{merged['output_tokens']:,} out, "
                f"est. cost (~{backend}): ${cost:.4f}"
            )
        # extract intentionally stops at graph.json + analysis; the report and
        # community labels are produced by `cluster-only` (or an agent's Step 5).
        # Point standalone users at it so communities get named (#1097).
        print(
            "[graphify extract] next: run "
            f"`graphify cluster-only {graphify_out.parent}` "
            "to generate GRAPH_REPORT.md and name communities"
        )

    elif cmd == "cache-check":
        # graphify cache-check <files_from> [--root <dir>]
        # Reads file paths (one per line) from <files_from>, checks semantic cache.
        # Writes:
        #   graphify-out/.graphify_cached.json   — already-cached nodes/edges/hyperedges
        #   graphify-out/.graphify_uncached.txt  — paths that need extraction
        # Stdout: "Cache: N hit, M miss"
        from graphify.cache import check_semantic_cache
        if len(sys.argv) < 3:
            print("Usage: graphify cache-check <files_from> [--root <dir>]", file=sys.stderr)
            sys.exit(1)
        files_from = Path(sys.argv[2])
        root = Path(".")
        i = 3
        while i < len(sys.argv):
            if sys.argv[i] == "--root" and i + 1 < len(sys.argv):
                root = Path(sys.argv[i + 1])
                i += 2
            else:
                i += 1
        files = [f for f in files_from.read_text(encoding="utf-8").splitlines() if f.strip()]
        cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(files, root)
        out = root / "graphify-out"
        out.mkdir(parents=True, exist_ok=True)
        if cached_nodes or cached_edges or cached_hyperedges:
            (out / ".graphify_cached.json").write_text(
                json.dumps({"nodes": cached_nodes, "edges": cached_edges, "hyperedges": cached_hyperedges},
                           ensure_ascii=False),
                encoding="utf-8",
            )
        (out / ".graphify_uncached.txt").write_text("\n".join(uncached), encoding="utf-8")
        print(f"Cache: {len(files) - len(uncached)} hit, {len(uncached)} miss")

    elif cmd == "merge-chunks":
        # graphify merge-chunks <chunk_glob_or_files...> --out <path>
        # Concatenates .graphify_chunk_*.json files written by semantic subagents.
        # Deduplicates nodes by id (first writer wins). Sums token counts.
        import glob as _glob
        if len(sys.argv) < 3:
            print("Usage: graphify merge-chunks <chunk_files...> --out <path>", file=sys.stderr)
            sys.exit(1)
        out_path: Path | None = None
        chunk_args: list[str] = []
        i = 2
        while i < len(sys.argv):
            if sys.argv[i] == "--out" and i + 1 < len(sys.argv):
                out_path = Path(sys.argv[i + 1])
                i += 2
            else:
                chunk_args.append(sys.argv[i])
                i += 1
        if not out_path:
            print("error: --out <path> required", file=sys.stderr)
            sys.exit(1)
        chunk_files: list[str] = []
        for arg in chunk_args:
            expanded = _glob.glob(arg)
            chunk_files.extend(sorted(expanded) if expanded else [arg])
        merged: dict = {"nodes": [], "edges": [], "hyperedges": [], "input_tokens": 0, "output_tokens": 0}
        seen_ids: set[str] = set()
        for cf in chunk_files:
            try:
                chunk = json.loads(Path(cf).read_text(encoding="utf-8"))
            except (json.JSONDecodeError, OSError) as exc:
                print(f"[graphify merge-chunks] warning: skipping {cf}: {exc}", file=sys.stderr)
                continue
            for n in chunk.get("nodes", []):
                if n.get("id") not in seen_ids:
                    seen_ids.add(n["id"])
                    merged["nodes"].append(n)
            merged["edges"].extend(chunk.get("edges", []))
            merged["hyperedges"].extend(chunk.get("hyperedges", []))
            merged["input_tokens"] += chunk.get("input_tokens", 0)
            merged["output_tokens"] += chunk.get("output_tokens", 0)
        out_path.parent.mkdir(parents=True, exist_ok=True)
        out_path.write_text(json.dumps(merged, ensure_ascii=False), encoding="utf-8")
        print(
            f"Merged {len(chunk_files)} chunks: {merged['nodes']} nodes, {len(merged['edges'])} edges, "
            f"{merged['input_tokens']:,} in / {merged['output_tokens']:,} out tokens"
        )

    elif cmd == "merge-semantic":
        # graphify merge-semantic --cached <path> --new <path> --out <path>
        # Merges cached semantic results with freshly-extracted chunk results.
        # Deduplicates nodes by id (cached entries take priority over new ones).
        if len(sys.argv) < 3:
            print("Usage: graphify merge-semantic --cached <path> --new <path> --out <path>", file=sys.stderr)
            sys.exit(1)
        cached_path: Path | None = None
        new_path: Path | None = None
        out_path2: Path | None = None
        i = 2
        while i < len(sys.argv):
            if sys.argv[i] == "--cached" and i + 1 < len(sys.argv):
                cached_path = Path(sys.argv[i + 1]); i += 2
            elif sys.argv[i] == "--new" and i + 1 < len(sys.argv):
                new_path = Path(sys.argv[i + 1]); i += 2
            elif sys.argv[i] == "--out" and i + 1 < len(sys.argv):
                out_path2 = Path(sys.argv[i + 1]); i += 2
            else:
                i += 1
        if not out_path2:
            print("error: --out <path> required", file=sys.stderr)
            sys.exit(1)
        empty: dict = {"nodes": [], "edges": [], "hyperedges": []}
        cached_data = json.loads(cached_path.read_text(encoding="utf-8")) if cached_path and cached_path.exists() else empty
        new_data = json.loads(new_path.read_text(encoding="utf-8")) if new_path and new_path.exists() else empty
        seen_ids2: set[str] = set()
        all_nodes: list[dict] = []
        for n in cached_data.get("nodes", []) + new_data.get("nodes", []):
            if n.get("id") not in seen_ids2:
                seen_ids2.add(n["id"])
                all_nodes.append(n)
        merged2 = {
            "nodes": all_nodes,
            "edges": cached_data.get("edges", []) + new_data.get("edges", []),
            "hyperedges": cached_data.get("hyperedges", []) + new_data.get("hyperedges", []),
        }
        out_path2.parent.mkdir(parents=True, exist_ok=True)
        out_path2.write_text(json.dumps(merged2, ensure_ascii=False), encoding="utf-8")
        print(f"Merged: {len(merged2['nodes'])} nodes, {len(merged2['edges'])} edges")

    elif Path(cmd).exists() or cmd in (".", "..") or cmd.startswith(("./", "../", "/", "~")):
        # User ran `graphify <path>` directly — treat as `graphify extract <path>`.
        # Common when following the PowerShell note in README (`graphify .`) or
        # copy-pasting skill invocations without the leading slash.
        sys.argv.insert(2, sys.argv[1])
        sys.argv[1] = "extract"
        main()
    else:
        print(f"error: unknown command '{cmd}'", file=sys.stderr)
        print("Run 'graphify --help' for usage.", file=sys.stderr)
        sys.exit(1)


if __name__ == "__main__":
    main()