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Author SHA1 Message Date
Safi 91f4d120b6 fix worktree hook crash, prune isolated code nodes, restore rationale-node prohibition 
- hooks.py: use git rev-parse --git-path hooks so install/status/uninstall
  work in linked worktrees where .git is a file not a directory (fixes #865)
- build.py: prune degree-0 code nodes after graph assembly to remove
  bundled/synthetic symbols with no connections (fixes #728)
- skill.md: restore explicit rule prohibiting file_type:"rationale" nodes
  and remind model to store rationale as an attribute instead (fixes #751)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-05-14 23:03:21 +01:00
Safi a01e0981ed fix #374 #401 #410 #413 #385: vscode install cmd, core.hooksPath, absolute cache root, Windows PATH docs, Kiro YAML colon 2026-04-17 08:33:02 +01:00
Safi d23ae1774d v2: hypergraph support - hyperedges in graph.json, shaded regions in HTML, report section 2026-04-05 23:18:25 +01:00
Safi e6fefa8a2c v2: semantic similarity edges, scored higher in surprising connections 2026-04-05 23:12:47 +01:00
Safi 0f11f6a32d v2: confidence scores on INFERRED edges, avg shown in report 2026-04-05 23:06:07 +01:00
Safi e8b8e2039d v2: fast --update for code-only changes, parallel AST+semantic, graphify claude install 2026-04-05 23:00:24 +01:00
Safi 0a31c0862b add git commit hook - auto-rebuilds graph after every commit 2026-04-05 22:40:34 +01:00
Safi 5617a7d285 watch: auto-rebuild graph on code changes without LLM, notify on doc/image changes 2026-04-05 20:13:26 +01:00
Safi fd2cc8d8a7 Surface all options post-run; wiki-first follow-ups; --update regenerates wiki 2026-04-05 17:07:57 +01:00
Safi ef06d7d8d9 Add --wiki export: agent-crawlable knowledge wiki from graph 2026-04-05 16:54:50 +01:00
Safi e98c1b6297 fix: HTML always generated by default in Step 6, not flag-gated 2026-04-05 14:22:42 +01:00
Safi a1be5abb24 refactor: dead imports, node_community helper, split to_html and call_tool 
- Remove unused shutil (cache.py), sys (ingest.py), inline import os (detect.py)
- Extract _node_community_map() helper - was copy-pasted 8 times across analyze.py + export.py
- Split to_html() 285-line monolith into _html_styles() + _html_script() + thin orchestrator
- Split serve.py call_tool() if/elif chain into per-tool handler functions + dispatch table
- Extract _find_node() helper shared across get_node and get_neighbors handlers

All 231 tests pass.
 2026-04-05 14:01:55 +01:00
Safi 0061b36c29 fix: 5 skill gaps - graphml usage, manifest timing, graph existence checks, no-viz clarity 
- Add --graphml to Usage table (was implemented but undocumented there)
- Remove early manifest save from --update merge step (Step 9 owns it; saving early meant failed pipelines left manifest ahead of graph)
- query/path/explain now check graph.json exists before running, with clear "run /graphify first" message
- --no-viz: clarify it skips both Obsidian vault and HTML (was contradictory)
 2026-04-05 13:50:07 +01:00
Safi c88528dfa3 perf: larger chunks + code-only fast path + timing estimates 
- Semantic extraction chunks: 12-15 → 20-25 files (fewer subagent round trips)
- Code-only corpora skip semantic dispatch entirely (AST covers it)
- Print estimated time before extraction so the wait feels intentional
 2026-04-05 13:42:11 +01:00
Safi fa702bd69f after pipeline, offer to guide user through the graph 2026-04-05 00:35:47 +01:00
Safi d7a54d7e14 fix critical install bug, add --graphml to pipeline, update changelog 2026-04-05 00:29:42 +01:00
Safi 8708333484 feat: vis.js HTML graph, token reduction benchmark, repo cleanup 
- Replace pyvis with custom vis.js renderer: node size by degree,
  click-to-inspect panel with clickable neighbors, search box,
  community filter, physics clustering by community
- HTML graph generated by default on every run (no --html flag needed)
- Token reduction benchmark auto-runs after every /graphify on corpora >5k words
- Fix 292 edge warnings: silently skip stdlib/external edges in build.py
- Fix build() to merge extractions before building (cross-extraction edges were dropped)
- Add 5 HTML renderer tests (223 total)
- Remove unnecessary files: lib/, tests/eval_attention.py, misplaced eval reports
- Add graphify-out/ and .graphify_*.json to .gitignore
- Bump version to 0.1.4, remove pyvis dependency
- README: token reduction as top-level selling point, vis.js in tech stack,
  graph.html in output listing, correct test count and install command
 2026-04-05 00:20:56 +01:00
Safi a7d1969f02 docs: update surprising connections description, test count 
style: replace all em dashes with hyphens

fix: explain hidden .graphify/ folder in skill output and README

fix: rename .graphify/ to graphify-out/ so output is visible by default
 2026-04-05 00:20:56 +01:00
Safi 258eff3e9f feat: composite surprise score — cross-type, cross-repo, community distance, peripheral→hub 2026-04-05 00:20:56 +01:00
Safi a7f910667d feat: GraphML export (--graphml flag) for Gephi and yEd 2026-04-05 00:20:56 +01:00
Safi 81a43f028f feat: 13-language AST support and token benchmark 
Java, C, C++, Ruby, C#, Kotlin, Scala, PHP via tree-sitter (13 total)
benchmark.py measures BFS subgraph tokens vs corpus tokens
5 skill bug fixes (cohesion crash, dead step, missing MCP tool)
 2026-04-04 18:56:38 +01:00
Safi 41e4e3576a security: SSRF protection, HTML escaping, path guards, encoding hardening 
- graphify/security.py (new): centralised security module
    - validate_url(): blocks file://, ftp://, data:, any non-http/https scheme
    - _NoFileRedirectHandler: re-validates redirect targets, blocks file:// redirects
    - safe_fetch(): streams response, 50MB hard cap, non-2xx raises, timeout
    - safe_fetch_text(): safe_fetch + UTF-8 decode with errors=replace
    - validate_graph_path(): resolves path, requires inside .graphify/, base must exist
    - sanitize_label(): strip control chars, cap 256, html.escape() — mirrors
      code-review-graph's _sanitize_name pattern
- graphify/ingest.py: _fetch_html() and _download_binary() now use safe_fetch*;
  ingest() validates URL scheme and wraps network calls in try/except;
  YAML frontmatter: newlines stripped from question before embedding
- graphify/extract.py: all 33 bare .decode() → .decode("utf-8", errors="replace")
  — non-UTF-8 source files degrade gracefully instead of crashing extraction
- graphify/export.py: sanitize_label() on all node labels and edge titles
  before pyvis embeds them in HTML output
- graphify/serve.py: _load_graph() validates graph_path via validate_graph_path()
  and wraps JSONDecodeError with recovery message; sanitize_label() on MCP
  text output
- graphify/detect.py: os.walk(..., followlinks=False) made explicit
- SECURITY.md (new): threat model, mitigations table, reporting process
- tests/test_security.py (new): 20 tests covering all security.py functions
 2026-04-04 18:56:38 +01:00
Safi 0b7460a9e3 perf+fix: parallel extraction, faster imports, bug fixes 
45x faster cluster import, 135x faster detect, parallel subagent extraction,
auto-exclude venvs/caches, suggest_questions fix, manifest fix, install CLI
 2026-04-04 18:56:38 +01:00
Safi e7a03a0539 feat: cache, multi-language extraction, MCP, memory feedback 
call-graph INFERRED edges, multi-language semantic extraction, SHA256 cache,
MCP stdio server with shortest_path, Q&A memory feedback loop
 2026-04-04 18:56:38 +01:00
Safi ce47198be1 feat: Claude Code skill, Obsidian vault, install, tests 
skill.md with full pipeline steps, Obsidian as default output (canvas, tags,
dataview, graph colors), two-command install, 71 tests, .gitignore, deps
 2026-04-04 18:53:43 +01:00