1. NEW: extract_markdown() — structurally indexes .md/.mdx files into the
knowledge graph. Headings become nodes, code blocks become nodes with
language tags, and nesting produces 'contains' edges. Zero new deps
(pure regex/line-by-line parsing, no tree-sitter needed).
2. FIX: collect_files() _EXTENSIONS was hardcoded and missing 18 extensions
that _DISPATCH already supported (.jsx, .mjs, .ex, .exs, .jl, .vue,
.svelte, .dart, .v, .sv, .sql, .f, .F, .f90, etc). Now uses
set(_DISPATCH.keys()) to stay automatically in sync.
3. Added deploy_guide.md test fixture and 6 new test cases.
4. Updated test_collect_files_from_dir to use dynamic extension set.
#700: _read_tsconfig_aliases() now handles // comments, /* */ block comments,
and trailing commas via a regex-based _strip_jsonc() helper. Tries plain
json.loads first, falls back to stripped parse, warns to stderr on failure
instead of silently returning {}.
#701 Bug A: removed startswith('.') filter from Svelte regex fallback so
aliased imports ($lib/, $partials/, @/) are no longer skipped.
#701 Bug B: fixed synthetic node IDs — source uses _make_id(str(path)),
target uses _make_id(str(normpath(parent/raw))) matching _extract_generic
and _import_js conventions so build_from_json no longer drops every edge.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Enables docs-only corpora to run full LLM extraction in CI without Claude Code.
Handles code-only, docs-only, and mixed corpora; --no-cluster for raw dumps.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
- Add Fortran support (26th language): .f/.F/.f90/.F90/.f95/.F95/.f03/.F03/.f08/.F08
via tree-sitter-fortran; capital-F files preprocessed with cpp -w -P
- Add graphify export {html,obsidian,wiki,svg,graphml,neo4j} CLI subcommands
- Add graphify query/path/explain CLI subcommands
- Reduce skill.md from 63KB to 47KB by replacing Python heredocs with CLI calls
- Extend to_html() with node_limit param for auto-aggregation on large graphs
- Add integration tests for all export/query/path/explain subcommands
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
shutil.which() first; falls back to sys.executable sibling Scripts/graphify.exe
so the hook works even when venv/Scripts is not on Codex's PATH.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Codex Desktop rejects hookSpecificOutput.additionalContext on PreToolUse.
hook-check is now a no-op — graph guidance reaches the agent via AGENTS.md/skill.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
#655 and #656 already fixed in cache.py and security.py.
#657: add rationale to file_type schema in all 12 skill variants; warn against inventing concept.
#658: add explicit chunk-merge step with token summation before save_semantic_cache.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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