#1118 — prune stale AST nodes on full re-extraction (#1116)
Stamps every AST-extracted node with _origin="ast" in extract(). On a
full rebuild _rebuild_code drops any AST-marked node absent from the
fresh output even when its source file survives, fixing stale symbols.
Backward-compat: marker-less nodes from pre-1118 graphs survive one
cycle then self-heal.
#1110 — stop reading images and PDFs as garbage in headless extract
Images route through per-backend vision payloads (base64/data-URI/bytes
for claude/openai/bedrock); non-vision backends get _strip_pixels for
graceful degradation. PDFs reuse pypdf. 5MB cap, 20-image chunk limit.
#1159 — Salesforce Apex extractor (.cls, .trigger)
Regex-based extractor: classes, interfaces, enums, methods, triggers,
SOQL/DML edges. No new dependency. Dispatched as .cls and .trigger.
#1107 — Azure OpenAI Service backend (--backend azure)
Uses AzureOpenAI SDK client (from existing openai package). Auto-detects
when AZURE_OPENAI_API_KEY + AZURE_OPENAI_ENDPOINT both set. Uses
max_completion_tokens (not deprecated max_tokens).
#1103 — live PostgreSQL introspection (--postgres DSN)
graphify extract --postgres "postgresql://..." introspects tables, views,
routines, and FK relations via information_schema (SERIALIZABLE READ ONLY).
Credentials sanitized on error. New graphify[postgres] extra (psycopg3).
Union-resolved llm.py conflict: Azure functions + bedrock images= param.
Fixed test_image_vision.py mock to accept timeout= kwarg (our #1112).
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Fixes#777. Relativize manifest keys, .graphify_root, and cache source_file fields on persist; re-anchor on load. In-memory callers still see absolute paths. Symlink round-trip fixed in follow-up commit 8f09326.
The post-commit hook passes `git diff --name-only HEAD~1 HEAD` as
changed_paths to `_rebuild_code`. That list includes deletions, and
`_rebuild_code` correctly identifies them (lines 352-367 in watch.py)
and evicts the stale nodes from the preserved set. The rebuilt graph
is intentionally smaller.
`_check_shrink` then refuses to overwrite the existing graph.json
because it only sees the node-count delta, not the cause. The guard
fires with "Refusing to overwrite — you may be missing chunk files
from a previous session. Pass --force to override."
Result: every commit that deletes a tracked file silently leaves stale
nodes in graph.json. The user must either pass --force (which also
disables the guard for legitimate failure modes) or manually re-run
`graphify update . --force` after delete-heavy commits.
Fix: thread a `had_explicit_deletions` flag from `_rebuild_code` into
`_check_shrink`. When the caller has declared the deletions, the
smaller graph is the expected outcome and the guard is skipped. The
guard remains intact for SILENT shrinkage — its actual purpose —
from failed semantic chunks or corrupted runs.
The fix is opt-in by design: callers that don't pass `changed_paths`
(e.g. the post-checkout full rebuild path) keep the old conservative
behavior. Only paths that explicitly track deletions get the bypass.
Tests added (tests/test_watch.py):
- `test_check_shrink_blocks_silent_shrink` — pre-existing behavior intact
- `test_check_shrink_allows_force_override` — pre-existing behavior intact
- `test_check_shrink_allows_explicit_deletions` — new: deletion bypass
- `test_check_shrink_allows_no_existing_data` — first-run case
- `test_check_shrink_allows_growth` — sanity
- `test_check_shrink_unlinks_tmp_on_refuse` — cleanup on refusal
- `test_check_shrink_keeps_tmp_when_deletions_declared` — no spurious unlink
- `test_rebuild_code_prunes_deleted_file_nodes` — end-to-end probe of the
exact scenario the post-commit hook triggers (git init, build, delete
one file, re-run with the deleted path in changed_paths, verify the
graph shrinks and the surviving file's nodes are preserved)
All 8 new tests pass; full test_watch.py + test_build.py + test_export.py
(74 tests) pass with no regressions.
Security: _is_sensitive now flags underscore-prefixed names (api_token.txt, oauth_token.json) by replacing \b with lookarounds; adds _SENSITIVE_DIRS check on parent path components (parts[:-1]) so .ssh/, secrets/, .aws/ directories are always skipped; aligns both patterns to (?![a-zA-Z]) for consistent underscore-after-keyword behavior (#920)
Fix: --wiki Relationships section always empty because _cross_community_links read community from node attrs (always None) instead of the communities dict; _god_node_article had the same bug and never linked to the owning community; fixed by building a node->community map in to_wiki() and threading it through (#925)
Fix: --watch now respects .graphifyignore; patterns loaded once at startup, handler checks _is_ignored before extension filter so node_modules/, .venv/, build/ churn no longer triggers rebuilds (#928)
Fix: C++ struct inheritance edges via base_class_clause; initialize base="" per iteration to prevent stale carryover (#915)
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Add .sh, .bash, .json to CODE_EXTENSIONS in detect.py so files reach extractor
- Fix test_detect_incremental manifest path collision with new .json extension
- Update test_watch to reflect .json/.sh are now watched extensions
- B-1: only emit source imports for paths that exist on disk
- J-1: replace stat()+read() with bounded read to eliminate TOCTOU
- J-3: move pair_count cap inside loop so it is honoured exactly
- J-4: namespace $ref/extends refs with "ref_" prefix to prevent ID collision
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
The rebuild lock file accumulated concatenated PIDs across post-commit
rebuilds without a separator, and was never removed when the rebuild
finished. Two practical consequences for users:
1. Downstream tooling that polls for `.rebuild.lock` to disappear before
doing post-rebuild work (publish scripts copying graph.html to a web
root, etc.) blocked forever / until its own timeout.
2. The accumulated digit string could not be parsed by humans or tooling
to find the owning PID.
The `_rebuild_lock` context manager now:
- Opens the lock file with `a+` so a non-acquiring caller does not
truncate the existing holder's PID.
- After flock acquisition, truncates and writes a single `<pid>\n` line
so external readers can `kill -0 $(cat .rebuild.lock)` to check
liveness.
- Unlinks the lock file in the finally block (only when *we* held the
lock), restoring the "signal-by-absence" convention users rely on.
Four regression tests added under `tests/test_watch.py` covering the
PID-with-newline payload, post-release unlink, no-accumulation across
sequential acquisitions, and the non-blocking-caller-does-not-clobber
invariant.
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Add a pre-cluster topology comparison fast path in update rebuilds so unchanged graphs short-circuit before clustering and report generation, preventing residual run-to-run community-count drift.
Co-authored-by: Cursor <cursoragent@cursor.com>
Make `graphify update` idempotent by skipping output rewrites when graph/report content is unchanged, add `update --no-cluster`, and preserve community IDs across runs via overlap-based remapping with deterministic partition inputs.
Co-authored-by: Cursor <cursoragent@cursor.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
Safi