* feat: detect circular import dependencies at file level
- Add find_import_cycles() to analyze.py
- Collapses symbol nodes to parent files, builds directed file graph
- Uses nx.simple_cycles() bounded by max_cycle_length (default 5)
- Deduplicates rotations, returns shortest cycles first
- Considers both imports_from and re_exports edges
Tested on a 976-file Next.js codebase: found 4 cycles including
a known utils↔barrel circular dependency and a 4-file API cycle.
* fix: resolve import-cycle merge blockers
- use source_file-only endpoint resolution (no label fallback)
- support Graph/DiGraph orientation via edge source_file
- return structured cycle records and include self-loops
- integrate Import Cycles section into GRAPH_REPORT.md
- expand cycle tests for real-schema IDs, undirected input,
missing source_file nodes, and non-import relations
- hooks.py: drop --path-format=absolute (added git 2.31), validate no newlines in path, anchor relative paths on repo root (#907)
- detect.py: seed save_manifest from existing manifest before loop so incremental callers don't erase untouched file entries (#917)
- cluster.py: drop round(..., 2) from cohesion_score so split threshold 0.05 fires correctly; add resolution param to _partition and cluster; add exclude_hubs_percentile to cluster with majority-vote reattachment (#919)
- report.py: format cohesion with :.2f for display
- __main__.py: wire --resolution and --exclude-hubs into extract and cluster-only commands (#919)
- C++ inheritance already written to disk by analysis agent (#915)
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Alembic/Flask-Migrate revisions, Django migrations, and protobuf/OpenAPI
generated files produce hundreds of degree-1 rationale nodes labeled as
'possible documentation gaps'. Their module docstrings are revision
annotations or boilerplate, not architectural rationale.
- Add _is_autogenerated_python() in extract.py detecting Alembic, Django
migrations, and generic DO-NOT-EDIT markers; skip module docstring only
- Function/class docstrings inside those files still extracted as normal
- report.py: exclude file_type=rationale nodes from isolated-node gaps
section — rationale nodes are degree-1 by construction; flagging them
as missing edges was always wrong
- 5 new tests covering Alembic, Django, protobuf, false-positive guard,
and function-docstring passthrough
- build/validate: accept NetworkX <=3.1 "links" key alongside "edges" (#212)
- __main__: skip version check during install/uninstall, deduplicate paths (#220)
- all file IO: explicit encoding="utf-8" to prevent crashes on Windows CJK locales (#204)
- hooks: add newline="\n" on write to prevent CRLF shebang breakage on Windows (#204)
- export: strip trailing .md from safe_name so "CLAUDE.md" doesn't become "CLAUDE.md.md" (#221)
- report: add Community Hubs navigation block so Obsidian vault stays connected (#221)
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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
Manoj Mishra