safishamsi caa6f9edb9 fix(extract): persist --no-gitignore instead of clobbering it (follow-up to #1979) ...

The PR always wrote gitignore=not no_gitignore into .graphify_build.json, so a
flag-less `graphify extract` after `--no-gitignore` reset it to True and the
git-ignored code silently disappeared again — the exact #1971 complaint. Write
False only when the flag is set (None = leave as-is, mirroring #1886 excludes),
and honor the persisted value for the run when the flag is absent.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

2026-07-18 12:09:08 +01:00

..

always_on

fix(skillgen): host-generic /graphify install guidance (#1530)

2026-06-29 10:01:06 +01:00

exporters

fix(export): close stored XSS + broken neighbor links in graph.html (#1838)

2026-07-13 17:48:26 +01:00

extractors

fix(resolution): repoint cross-extension re-exports without leaking an absolute path (#1814)

2026-07-18 12:04:23 +01:00

skills

fix(skill): utf-8 encoding in query reference snippets (#1619 A2)

2026-07-03 11:37:22 +01:00

__init__.py

feat: self-improving work-memory — save-result outcomes + graphify reflect (#1441)

2026-06-24 11:43:13 +01:00

__main__.py

fix: add --no-gitignore extraction opt-out

2026-07-18 12:05:00 +01:00

_minhash.py

perf/fix: replace datasketch with pure-numpy MinHash; memoize detect ignore checks

2026-06-10 15:50:38 +01:00

affected.py

feat(ruby/affected): mixes_in edges for include/extend/prepend + method-bound callers in affected (#1668, #1669)

2026-07-05 11:41:18 +01:00

analyze.py

fix: treat .cjs (explicit CommonJS) as a code extension

2026-07-15 13:13:30 +01:00

benchmark.py

Honour GRAPHIFY_OUT end-to-end, not just in the path guards (#1423)

2026-06-22 21:15:51 +01:00

build.py

fix(resolution): repoint cross-extension re-exports without leaking an absolute path (#1814)

2026-07-18 12:04:23 +01:00

cache.py

fix(cache): key file_hash stat-index memo by salt, not absolute path (#1989)

2026-07-18 12:03:34 +01:00

callflow_html.py

Relativize hyperedge source_file and honour GRAPHIFY_OUT everywhere (#1418, #1423)

2026-06-22 17:02:29 +01:00

cargo_introspect.py

fix(cargo): honor package = "..." rename when resolving internal deps (#1858)

2026-07-14 13:19:16 +01:00

cli.py

fix(extract): persist --no-gitignore instead of clobbering it (follow-up to #1979)

2026-07-18 12:09:08 +01:00

cluster.py

fix(cluster): detect stale community labels on cluster-only re-cluster

2026-07-01 11:52:50 +01:00

command-kilo.md

feat: add Kilo Code support (#512)

2026-06-01 16:05:07 +01:00

dedup.py

fix(dedup): deterministic collision survivor + bare-file definer (#1851 followup)

2026-07-14 13:51:42 +01:00

detect.py

fix: add --no-gitignore extraction opt-out

2026-07-18 12:05:00 +01:00

diagnostics.py

fix(llm): move the unverifiable-node flag to a real, consumed field (follow-up to #1949)

2026-07-17 00:09:02 +01:00

export.py

fix(io): write graph.json and manifest.json atomically

2026-07-16 23:42:47 +01:00

extract.py

fix(resolution): repoint cross-extension re-exports without leaking an absolute path (#1814)

2026-07-18 12:04:23 +01:00

file_slice.py

Slice oversized text documents so the whole file is extracted (#1369)

2026-06-18 01:55:56 +01:00

global_graph.py

fix(io): route the remaining graph/manifest writers through the atomic helper (follow-up to #1952)

2026-07-16 23:48:07 +01:00

google_workspace.py

Harden Google Workspace gws exports (#772)

2026-05-07 20:07:57 +01:00

hooks.py

Fix spurious hooksPath warning and register graph.json merge driver

2026-07-15 00:41:36 +01:00

ids.py

Unify node-ID normalization into a single source of truth (#1378)

2026-06-18 22:55:44 +01:00

ingest.py

feat: self-improving work-memory — save-result outcomes + graphify reflect (#1441)

2026-06-24 11:43:13 +01:00

install.py

feat(hook): opt-in strict PreToolUse guard + stop crying wolf (#1840)

2026-07-17 17:10:41 +01:00

llm.py

fix(llm): move the unverifiable-node flag to a real, consumed field (follow-up to #1949)

2026-07-17 00:09:02 +01:00

manifest_ingest.py

Parse package manifests into canonical package nodes + depends_on edges (#1377)

2026-06-19 10:25:09 +01:00

manifest.py

perf+fix: parallel extraction, faster imports, bug fixes

2026-04-04 18:56:38 +01:00

mcp_ingest.py

fix(ids): node IDs include the full repo-relative path (#1504, #1509)

2026-06-28 16:57:00 +01:00

multigraph_compat.py

feat(multigraph): add runtime compatibility probe (#956)

2026-05-22 13:22:51 +01:00

pascal_resolution.py

fix(extract): scope Pascal/Delphi call resolution + resolve inherited calls across files (#1739)

2026-07-09 00:32:21 +01:00

paths.py

fix(io): route the remaining graph/manifest writers through the atomic helper (follow-up to #1952)

2026-07-16 23:48:07 +01:00

pg_introspect.py

fix(pg_introspect): emit FK DDL before function stubs so unparseable routines can't drop references edges (#1854)

2026-07-16 16:36:49 +01:00

prs.py

fix(prs): decode gh/git/claude output as UTF-8, not the Windows cp1252 codec

2026-07-18 12:03:47 +01:00

querylog.py

fix(querylog): make the query log opt-in, off by default (#1797)

2026-07-12 10:36:00 +01:00

reflect.py

fix(reflect): layout-ordered source resolution for overlay staleness (#1558)

2026-06-30 12:57:33 +01:00

report.py

fix(report): don't emit dangling [[_COMMUNITY_*]] wikilinks by default (#1712)

2026-07-07 10:57:52 +01:00

resolver_registry.py

feat(ruby): type-aware member-call resolution via a resolver framework (#1499)

2026-06-29 09:40:22 +01:00

ruby_resolution.py

fix(extract): route .rake files to the Ruby extractor + resolution (#1784)

2026-07-11 11:31:47 +01:00

scip_ingest.py

feat(multigraph): add runtime compatibility probe (#956)

2026-05-22 13:22:51 +01:00

security.py

test(security): cover GRAPHIFY_MAX_GRAPH_BYTES parsing; clarify unit docstring

2026-07-08 01:03:28 +01:00

semantic_cleanup.py

fix(merge-chunks): validate untrusted subagent chunk JSON before merging

2026-07-16 23:36:49 +01:00

serve.py

perf(serve): collapse T+1 per-term scoring passes into one traversal

2026-07-15 15:07:25 +01:00

skill-agents.md

fix(cache): key semantic cache on the extraction prompt (#1939)

2026-07-16 16:38:12 +01:00

skill-aider.md

fix(cache): scope semantic cache writes to extracted files (#1757)

2026-07-13 00:35:32 +01:00

skill-amp.md

fix(cache): key semantic cache on the extraction prompt (#1939)

2026-07-16 16:38:12 +01:00

skill-claw.md

fix(cache): key semantic cache on the extraction prompt (#1939)

2026-07-16 16:38:12 +01:00

skill-codex.md

fix(cache): key semantic cache on the extraction prompt (#1939)

2026-07-16 16:38:12 +01:00

skill-copilot.md

fix(cache): key semantic cache on the extraction prompt (#1939)

2026-07-16 16:38:12 +01:00

skill-devin.md

fix(cache): scope semantic cache writes to extracted files (#1757)

2026-07-13 00:35:32 +01:00

skill-droid.md

fix(cache): key semantic cache on the extraction prompt (#1939)

2026-07-16 16:38:12 +01:00

skill-kilo.md

fix(cache): key semantic cache on the extraction prompt (#1939)

2026-07-16 16:38:12 +01:00

skill-kiro.md

fix(cache): key semantic cache on the extraction prompt (#1939)

2026-07-16 16:38:12 +01:00

skill-opencode.md

fix(cache): key semantic cache on the extraction prompt (#1939)

2026-07-16 16:38:12 +01:00

skill-pi.md

fix(cache): key semantic cache on the extraction prompt (#1939)

2026-07-16 16:38:12 +01:00

skill-trae.md

fix(cache): key semantic cache on the extraction prompt (#1939)

2026-07-16 16:38:12 +01:00

skill-vscode.md

fix(cache): key semantic cache on the extraction prompt (#1939)

2026-07-16 16:38:12 +01:00

skill-windows.md

fix(cache): key semantic cache on the extraction prompt (#1939)

2026-07-16 16:38:12 +01:00

skill.md

fix(cache): key semantic cache on the extraction prompt (#1939)

2026-07-16 16:38:12 +01:00

symbol_resolution.py

fix(resolve): test mocks no longer erase the real cross-file call graph (#1553)

2026-06-30 16:59:16 +01:00

transcribe.py

Honour GRAPHIFY_OUT end-to-end, not just in the path guards (#1423)

2026-06-22 21:15:51 +01:00

tree_html.py

Harden HTML output against U+2028 XSS + two crash-on-adversarial-input fixes (#1357)

2026-06-17 10:46:19 +01:00

validate.py

Fix: validate_extraction crashes on non-hashable node id / edge endpoint

2026-06-24 08:54:11 +01:00

watch.py

fix: add --no-gitignore extraction opt-out

2026-07-18 12:05:00 +01:00

wiki.py

fix(wiki): portable relative markdown links so navigation works outside Obsidian (#1444)

2026-06-27 10:19:15 +01:00