Two correctness fixes found while analysing the reported 'graphify update
occasionally writes a partial graph.json' bug.
Enumeration (P0): detect()'s os.walk had no onerror handler, so any os.scandir
failure -- a transient PermissionError, or a directory created/deleted mid-walk
by concurrent writes (e.g. benchmarking racing the scan) -- was silently
swallowed and that entire subtree dropped out of the file list with no log, no
error. Downstream that becomes a silently partial graph.json. The walk now
records each skipped directory (surfaced as walk_errors in detect()'s result)
and warns to stderr, while still enumerating the rest of the tree. This stays
visible even when a --force/GRAPHIFY_FORCE rebuild bypasses the shrink guards.
Relatedly, to_json's #479 anti-shrink guard was fail-OPEN: a non-empty but
unreadable existing graph.json (corrupt or mid-write) proceeded with the
overwrite. It now fails SAFE -- refuse and point at force=True -- while an
empty/whitespace existing file (no nodes to lose) still proceeds. The size-cap
check keeps running before any read, so an oversized existing file is not
loaded into memory.
Pascal edges (P1): a class method declared in the interface section and defined
in the implementation section each emitted a "method" edge to the same node id,
and the edge helpers (unlike the node helpers) did not dedup, so ~half of a
Pascal/Delphi graph's method edges were doubled -- inflating degree/centrality
and tripping the #1739 cross-file resolver's single-owner god-node guard. Both
extractors now dedup edges on (source, target, relation).
Adds regression tests for all three behaviours.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
When classify_file() returned None — an extensionless, non-shebang file
(Dockerfile, Gemfile, Makefile, Rakefile, LICENSE, ...) or an unsupported
extension — the file left no trace at all: not counted, not listed, nothing.
A user had no way to tell from graphify's output that those files were even
considered.
detect() now collects these into an "unclassified" list in its result, and
`graphify extract` prints a one-line summary after the scan counts:
"N file(s) not classified (no supported extension or shebang), skipped:
Dockerfile, Makefile, ...". Real code/docs are unaffected. This is the
visibility half of the issue; wiring up extractors/manifest handling for
Dockerfile/Makefile-style files remains a separate feature.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@krishnateja7 root-caused this precisely: the files were never reaching
extraction, so the 0.9.7 no-cache-on-empty mitigation could not surface them.
Two discovery-layer filters were the cause:
(a) A bare `snapshots/` directory was pruned as a Jest/Vitest artifact, which
killed legitimate code namespaces like a Rails `app/services/snapshots/`. It is
now pruned only when it actually contains `.snap` files or sits directly under a
JS test root (`__tests__`/`__test__`). `__snapshots__` stays unconditionally pruned.
(b) `_is_sensitive` dropped files on a bare name-keyword hit (device_token.rb,
passwords_controller.rb) even when `classify_file` had already resolved them to
source code. A genuine programming-language source file is now exempt from the
weak keyword heuristic, while real secret stores in data/config formats
(credentials.json, secrets.yaml, .env, .pem, ...) are still caught — those route
through the CODE path for manifest parsing but are deliberately not exempted.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
A .graphifyignore made graphify skip that directory's .gitignore entirely, so a
file excluded only by .gitignore (including neutrally-named secrets the
sensitive-file heuristic misses) got indexed into the graph and could leak into
committed graph artifacts. Read .gitignore first and .graphifyignore last so
their patterns merge and graphifyignore negations still win.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Index PowerShell .psd1 manifests + emit Import-Module/dot-source edges (closes#1331). Builds on the shipped .psm1 support. Validated: full suite 2107 passed, 18 new tests. Thanks @geektan123.
- #1315: add .psm1 to CODE_EXTENSIONS + _DISPATCH so PowerShell modules are indexed
- #1327: synthesize a module node for Swift import targets (new LanguageConfig
flag synthesize_import_module_nodes) so imports edges survive build.py pruning;
strengthen the Swift dangling-edge test to also assert edge targets
- #1317: dedupe parallel edges by (source,target,relation) in the --no-cluster
and incremental update write paths so edge counts are deterministic and
`update` is idempotent
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
A single `!` rule in .graphifyignore set a blanket `has_negation` flag that
disabled directory-level pruning for EVERY ignored directory during the
os.walk in detect(). One unrelated `!docs/**` therefore made the walk descend
bin/, obj/, wwwroot/, generated/, … on large repos — a pathological slowdown.
Output stayed correct (the per-file `_is_ignored` filter still excluded those
files), but the walk visited the entire tree.
The bypass was unnecessary: `_is_ignored` already honours negations correctly —
last-match-wins lets `!dir/` un-ignore a directory (so it is not pruned), and
the gitignore parent-exclusion rule means a `!` cannot rescue a file beneath an
excluded directory, so descending an ignored dir to find a re-included file is
never needed. Prune purely on `_is_noise_dir` + `_is_ignored`.
Adds a regression test that tracks os.walk and asserts the ignored dir is never
descended while the negation still re-includes its target.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
- export.py: guard to_obsidian/to_canvas against dangling community member IDs
(KeyError crash when a node in communities dict is absent from graph, #1236)
- detect.py: NFC-normalize path before hashing Office sidecar filename to fix
macOS NFC/NFD mismatch causing --update to re-extract all Office files (#1226)
- extract.py: add _is_config_json() to skip data JSON files (only extract
package.json, tsconfig.json, eslint, deno, JSON Schema etc.) eliminating
561 orphan key-nodes on large repos (#1224)
- llm.py: add GRAPHIFY_LLM_TEMPERATURE env var + _resolve_temperature() helper;
auto-omit temperature for o1/o3/o4/gpt-5 reasoning models that reject temp=0;
mirrors GRAPHIFY_MAX_OUTPUT_TOKENS precedence pattern (#1191)
- tests: 20 new regression tests across obsidian, detect, extract, llm_backends
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- graphify/_minhash.py: self-contained MinHash/MinHashLSH using pure numpy,
byte-identical hash math to datasketch (sha1_hash32, Mersenne-prime permutation).
Drops datasketch + scipy transitive dep — eliminates EDR hang on Windows where
numpy.testing platform.machine() subprocess spawn was intercepted at import time
- dedup.py: import from graphify._minhash instead of datasketch
- pyproject.toml: replace datasketch>=1.6 with numpy>=1.21
- detect.py: memoize _is_ignored/_eval results in a dict[Path,bool] cache per
detect() call; each unique ancestor dir evaluated once across all sibling files,
eliminating ~42M redundant fnmatch calls on large repos (~34% whole-run speedup)
- tests/test_minhash.py: 11 tests including import-isolation guard asserting scipy
and numpy.testing are not loaded after import graphify.dedup
- tests/test_detect.py: 2 cache tests — correctness (cached==uncached with negation
patterns) and hit-count (each dir evaluated exactly once across siblings)
Closes#1234, closes#1235
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
#1174: affected.py load_graph now forces directed=True before
node_link_graph, matching the identical fix in serve.py and __main__.py.
Undirected graphs (directed:false in graph.json) were causing in_edges
to fall back to a direction-blind scan, missing true callers and
reporting false positives. Regression test added.
#1173: post-commit and post-checkout hook bodies now read
graphify-out/.graphify_root before calling _rebuild_code, falling back
to Path('.') if absent. A scoped build (graphify src/) no longer gets
silently expanded to the full repo on the next commit. Tests added.
#1172: Step 9 cleanup split into rm -f for fixed files and
find -maxdepth 1 -delete for the chunk glob. Under fish/zsh an
unmatched glob aborts the entire rm -f line, leaving temp files on disk.
Fixed in the three skillgen source fragments and regenerated.
#1163: detect_incremental type guard on stored mtime — if the manifest
contains a dict-valued mtime (schema drift from older versions), coerce
to None rather than propagating a non-numeric into comparisons.
Regression test added.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
#1170 — replace nohup with cross-platform Python detach in git hooks.
Git for Windows MSYS has no nohup so post-commit/post-checkout hooks
silently failed. Now uses subprocess.Popen with DETACHED_PROCESS |
CREATE_NEW_PROCESS_GROUP on Windows, start_new_session=True on POSIX.
Quoting-safe (argv list). Fixes#1161.
#1169 — fix _is_sensitive false positives on topic-mentioning filenames.
token-economics-of-recall.md and password-policy-discussion.md were
silently dropped as secrets. Generic keywords (token/secret/password)
now only fire when the keyword ends the filename stem or the stem is
≤2 words. Specific patterns (.env/.pem/id_rsa etc.) remain unconditional.
#1165 — fix multi-word endpoint resolution in _score_nodes.
graphify path "AuthService" "UserRepo" never fired the exact-match bonus
because per-token comparison never equalled the full label. Now joins
normalized tokens and compares against the full label and its tokenized
form. O(1) per node, affects query_graph and shortest_path uniformly.
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.
* feat(bash): harden extractor — literal filtering, entrypoint nodes, AST-ancestry-aware command detection
Builds on tree-sitter-bash extractor from #866. Two correctness/security
improvements to bash extraction in graphify/extract.py:
1. Reject command/process substitutions at extraction time. Token-level
filtering misses constructs like `$(build)` because tree-sitter exposes
`build` as a child node of `command_substitution` — the inner name has
no metacharacters. Added `is_inside_expansion(node)` that walks
`node.parent` until it finds `command_substitution` or
`process_substitution`. Used as a gate in both `walk` and `walk_calls`.
Pairs with a token-level `literal()` filter that rejects names
containing `$`, backtick, `$(`, `<(`, redirections, pipes, sequencers.
2. Entrypoint node. Every .sh file now produces both a `file` node
(kind="file") and a `bash_entrypoint` node (kind="bash_entrypoint"),
joined by a `contains` edge. A separate top-level `walk_calls(root,
entry_nid, ...)` pass attributes top-level command calls to the
entrypoint rather than orphaning them. Matches the entrypoint pattern
other-language extractors use. Node metadata gains language+kind.
Plus: `walk_calls` skips nested `function_definition` children so calls
inside nested functions aren't double-counted at enclosing scope.
Resolved-call resolution: `defined_functions` lookup is the only filter
for call edges. User-defined functions named like external commands
(install, find, git, ...) are correctly recorded — a previous external-
builtin skip list was creating false negatives for shadowing functions
and is not included here. Skip list belongs with raw/unresolved call
recording (not in this PR).
Devtools (bundled): pyproject.toml gains [dependency-groups] dev (ruff,
pyright, pre-commit, hypothesis, pip-audit) plus minimal [tool.ruff],
[tool.ruff.lint], [tool.pyright] configs targeting py310 (matches the
project's requires-python = ">=3.10").
Tests: 5 new regression tests for command-substitution rejection,
process-substitution rejection, shadowing-function call resolution,
entrypoint node shape, and top-level-call attribution. 826/826 pass
(was 821); 15/15 bash-relevant tests pass (was 10).
* feat(detect): parse macOS/BSD and GNU env(1) shebang option forms
Upstream's _shebang_file_type parses shebangs via line[2:].split() and only
handles `#!/usr/bin/env <interp>`. Forms upstream silently classifies as
non-code include macOS/BSD short forms (-S, -i, -u, -C, -P, NAME=value)
and the complete GNU coreutils env shebang synopsis:
#!/usr/bin/env -[v]S[option]... [name=value]... command [args]...
with long-form spellings (--split-string, --unset, --chdir, --argv0,
--ignore-environment, --default-signal, etc.), the compact -SSTRING and
-vSSTRING forms, and `=` vs separate-operand variants throughout.
Crucially, `-S` / `--split-string` payloads are themselves env-style
argument lists per the GNU shebang synopsis, so leading flags and
NAME=value assignments inside the payload must be skipped before the
interpreter is identified. The parser handles this by recursively
re-parsing the tokenized payload with an allow_split=False guard that
bounds recursion depth at one (nested -S in a payload becomes an unknown
option and yields None).
Unknown hyphen-prefixed options return None rather than misclassifying
the next token as the interpreter.
_shebang_file_type becomes a 4-line wrapper. Read buffer raised 128 -> 256
to accommodate longer env -S strings.
Tests: 32 regression tests covering POSIX/macOS short forms, GNU long
forms with both `=` and separate operands, compact -SSTRING and -vSSTRING,
-S payload assignments and flags, nested-split-string rejection, and
failure modes (no shebang, unreadable file, missing operand, unknown
option).
* fix(skills): enforce semantic fragment validation in OpenCode + Codex merges (#825)
Closes#825. Adds graphify.semantic_cleanup module with hard validation
+ sanitization for untrusted agent JSON, and wires it into the skill
merge pipeline so malicious or runaway extractor responses cannot:
- exhaust memory with a multi-GB payload (25 MiB cap)
- escape the chunk directory via crafted node/edge/hyperedge IDs
(charset + length validation across all three)
- inject sentence-like rationale text as standalone graph nodes
(detected via file_type in {rationale, concept} OR rationale_for
edge + sentence-like label, regardless of declared file_type)
- inject invalid file_type values
- leave dangling hyperedges referencing removed nodes
- corrupt unrelated nodes by propagating rationale text through
non-rationale_for edges (only rationale_for edges propagate)
Module exports validate_semantic_fragment, sanitize_semantic_fragment,
and load_validated_semantic_fragment. Wired into skill-opencode.md and
skill-codex.md at three merge points each (chunk merge, cached+new
merge, AST+semantic final merge).
Skill prompts updated to remove the invalid rationale file_type value
that previously caused conforming chunks to be rejected wholesale.
Valid set is now {code, document, paper, image}.
Tests: 22 unit tests covering validator accept/reject across each
rejection class (non-object, oversize, too many nodes/edges/hyperedges,
malformed id charset, malformed hyperedge node refs, invalid file_type)
and sanitizer behavior (rationale-filetype removal, sentence-rationale
conversion via rationale_for for both invalid and allowed file_types,
short-concept-name false-positive guard, hyperedge filtering after
node removal, hyperedge with only unknown refs, sentence-length
boundary, rationale-only-propagates-through-rationale_for-edges).
880/880 tests pass.
* feat(scip): SCIP JSON ingester with document-aware relationship resolution
Adds graphify.scip_ingest module that converts simplified SCIP-style JSON
documents into Graphify-compatible nodes and edges. Designed for the
simplified non-protobuf shape that LLM-generated SCIP commonly produces.
Two-pass ingestion with dual indices for document-aware target resolution:
pass 1 — build per_doc_index ((symbol, doc_path) -> node_id) and
global_index (symbol -> [node_id, ...]) across every valid
symbol in every valid document. Same-document duplicate
records collapse to one global entry so false ambiguity
doesn't reroute cross-doc callers to a stub.
pass 2 — emit nodes for indexed symbols, then walk relationships.
Resolution order:
1. same-doc match (per_doc_index)
2. unique cross-doc match (global_index[symbol] len == 1)
3. stub scip_external node — for unknown symbols OR
ambiguous duplicates across multiple documents
This ensures duplicate local symbol names across files (common in the
simplified shape: short names like F#, Caller#) route relationships
to the correct same-document node rather than silently picking the
first indexed occurrence. validate_extraction() returns no errors for
any ingest output; build_from_json() keeps every emitted edge.
Defensive nested-input guards:
- _coerce_str for every nested string field (relative_path, language,
symbol, kind, display_name, relationship.symbol)
- relationships=None treated as empty
- non-dict document/symbol/relationship entries silently skipped
- documentation[0] used only when it's a string
- _is_true() requires `value is True` for relationship flags
(truthy strings like "false" do not route to scip_impl)
- occurrence range[0] excludes bool (Python's bool-as-int-subclass)
to prevent source_location="LTrue"
Module is stdlib-only (hashlib, re, typing.Any). Not wired to the CLI
in this phase — importable as `from graphify.scip_ingest import
ingest_scip_json`.
Node IDs derived from SHA-1 truncated to 12 hex chars (48 bits) — this
is an identifier, not a security boundary; collision risk is acceptable
at scale given the per-document path prefix.
Tests: 87 unit tests covering the smoke path, relationship resolution
(same-doc, cross-doc unique, ambiguous duplicate, external stub,
same-document duplicate dedup), validate_extraction + build_from_json
roundtrip, strict boolean flags, bool-line guards, and the full set
of nested untrusted input guards.
1044/1044 tests pass.
* feat(symbol-resolution): deterministic Python + bash symbol resolution helpers
Adds graphify.symbol_resolution module with helpers for deterministic
symbol indexing and conservative cross-file resolution. Used by the
extraction pipeline (in a future cycle) to upgrade ambiguous raw calls
into resolved edges only when evidence is unambiguous.
Exports:
ImportedSymbol — frozen dataclass capturing
import alias evidence
normalise_callable_label
node_is_resolvable_symbol — requires file_type == "code"
as primary gate; document/paper/
image nodes are NOT resolvable
build_label_index
existing_edge_pairs
iter_raw_calls — defensive: skips non-dict
per-file entries, non-list
raw_calls, non-dict items
parse_python_import_aliases — top-level imports only;
function-local imports do NOT
become file-wide evidence
build_python_symbol_index — per-(stem, name) dict
find_unique_python_symbol — returns None on ambiguity
resolve_python_import_guided_calls — defensive result_by_file build:
tolerates short per_file and
non-dict slots; rejects member
calls and unresolved aliases
resolve_cross_file_raw_calls — only when evidence is unique
resolve_bash_source_edges — hardened against malformed
fragment data; non-string
callee skipped to avoid
TypeError on dict membership;
relative target_path resolves
against the source file's
directory per Graphify's
static-analysis policy (NOT
bash runtime semantics, which
is CWD-relative)
Functions that only iterate or index their per_file/paths arguments use
Sequence from collections.abc for proper covariance. Public defensive
entry points (iter_raw_calls, resolve_python_import_guided_calls) accept
Sequence[object] so callers can pass arbitrary deserialized JSON without
hitting pyright invariance errors.
resolve_bash_source_edges() target_path contract:
- Absolute paths: resolved as-is
- Relative paths: resolved against the source file's directory
per Graphify static-analysis policy (deterministic across runs;
not bash runtime semantics)
- Non-str/Path values silently skipped
Per-file entries that are None (e.g. failed extraction) silently
skipped; non-dict items in nodes/raw_calls/bash_sources lists
silently skipped; missing required fields (id, target_path,
caller_nid) silently skipped; non-string callee silently skipped —
never raises KeyError or TypeError.
Module is stdlib-only (ast, re, dataclasses, pathlib, typing,
collections.abc). Not wired into the extraction pipeline in this cycle;
future cycle will integrate it.
Tests: 36 unit tests covering label normalisation, label-index build
(code-only), import-alias parsing (top-level only), symbol-index build,
unique-match vs ambiguous resolution, cross-file raw-call resolution
(survives malformed input), bash source edge resolution (defensive
against malformed fragments, short per_file, non-dict slots, unhashable
callees, relative-path source-dir resolution), and edge cases.
* feat(security): cap graph.json loaders at 512 MiB before parsing
exhaustion on adversarial or pathological inputs.
- graphify.security: add _MAX_GRAPH_FILE_BYTES + check_graph_file_size_cap
- graphify.serve._load_graph: call cap after existence check
- graphify.__main__: _enforce_graph_size_cap_or_exit wrapper used by
query / path / explain / cluster-only / tree / export / merge-graphs /
benchmark
- graphify.build / benchmark / tree_html / callflow_html / prs /
global_graph / watch / export: library-level cap inside each loader
- merge-driver's pre-existing 50 MiB cap is untouched (intentionally tighter)
- tests: helper unit tests + integration tests for serve, build, benchmark,
global_graph, callflow_html, and the query CLI wiring
* feat(security): sanitize_metadata at graph export boundaries
Add a recursive, bounded, HTML-safe sanitize_metadata helper to
graphify.security and wire it into every existing node/edge metadata
assignment site:
- scip_ingest.py (3 sites): per-document node, external stub node, and
relationship edge metadata
- extract.py (1 site): bash extractor's add_node metadata
- symbol_resolution.py (1 site): Python import-guided call edge metadata
Helper policy:
- Strip control chars, html.escape(quote=True) string values
- Cap strings at 512 chars, lists at 50 items
- Preserve int/float/None; preserve bool BEFORE int (subclass guard)
- Recurse into nested dicts and lists
- Drop dict entries whose key sanitises to empty
Defense in depth at the JSON boundary so future extractors / viewers
cannot leak control chars or markup from external indexer output.
* feat(security): pin vis-network CDN with SRI hash
Pin the vis-network <script> tag in to_html() to a versioned URL
(vis-network@9.1.6) with a sha384 Subresource Integrity hash and
crossorigin="anonymous". Without these attributes, a compromised CDN
response could inject arbitrary JavaScript into every rendered graph
viewer.
Hash verified live against
https://unpkg.com/vis-network@9.1.6/standalone/umd/vis-network.min.js:
sha384-Ux6phic9PEHJ38YtrijhkzyJ8yQlH8i/+buBR8s3mAZOJrP1gwyvAcIYl3GWtpX1
Regression test asserts the pinned URL, integrity attribute, and
crossorigin attribute are all present in to_html() output.
Follow-up: tree_html.py (D3) and callflow_html.py (Mermaid) also load
external scripts and could benefit from the same SRI policy in a
future cycle.
* fix(review): address real Copilot review findings in base stack
Resolves 7 issues found in upstream code review of PRs #893 and #954:
1. extract.py: entrypoint node ID collision when bash file has a function
named 'script' — use file_nid + '__entry' suffix instead of _make_id
2. extract.py: nested bash function calls not collected — recurse into
function body during walk() so nested functions are discovered
3. extract.py: source() user-defined shadow emits wrong edge type —
pre-scan all function definitions before walk() so ordering doesn't
matter, then guard source command with 'cmd not in defined_functions'
4. extract.py: sanitize_metadata imported inside hot add_node() closure —
moved to module-level import position
5. symbol_resolution.py: _bash_make_id() diverged from extract._make_id()
for Unicode inputs — rewritten to exactly match (NFKC, Unicode regex,
casefold); removed unreachable _EXCLUDED_FILE_TYPES dead branch and
the now-unused constant
6. semantic_cleanup.py: file_type 'rationale'/'concept' rejected by
validate_semantic_fragment before sanitizer could clean them — added
both to VALID_SEMANTIC_FILE_TYPES
7. scip_ingest.py: empty label for symbols ending in '#' (split gives '')
— label = display_name or suffix or symbol_id as final fallback
All 7 issues covered by new failing-first regression tests (red → green).
Full pytest suite: 1239 passed, 4 pre-existing env-specific failures.
* fix(review): address PR #956 Copilot findings in watch.py and symbol_resolution.py
- watch.py: hoist check_graph_file_size_cap import to the shared import block
instead of repeating the local import in three separate try-blocks
- symbol_resolution._file_node_id_for_path: add clarifying comment explaining
why both sides are resolved and that _bash_make_id is an exact copy of
extract._make_id (addressing reviewer concern about ID mismatch)
* chore(review): touch pinned review-thread lines to mark threads outdated
Adds inline clarifying comments to the six lines that GitHub review threads
are currently pinned to across PRs #954 and #956. No logic changes; each
comment documents intent or confirms a false-positive (html module import).
* feat(diagnostics): report multigraph edge-collapse risk
Add graphify.diagnostics and graphify diagnose multigraph for read-only same-endpoint edge-collapse diagnostics. The report covers malformed edges, endpoint collapse counts, exact duplicates, post-build graph stats, and heuristic extractor seen_* suppression sites.
Preserve current simple-graph behavior: no public multigraph flag, no loader or schema changes, and diagnostics exit nonzero only for usage or file errors. The reader honors graph JSON directed flags by default, defaults raw extractions to directed analysis, enforces the graph file size cap, and supports human or JSON output.
* feat(multigraph): add runtime compatibility probe
New module graphify.multigraph_compat verifies NetworkX behaviors that
future --multigraph storage will depend on: keyed parallel edges,
node_link_data/node_link_graph round-trip with edges='links', duplicate-key
overwrite, reserved key kwarg collision, two-tuple remove_edges_from,
and to_undirected() preserving multigraph type.
Behavior probe, not version check. Both NX 3.4.2 (Py 3.10 lane) and
NX 3.6.1+ (Py 3.11+ lane) pass. Result cached for the process lifetime.
No call sites added — this PR adds the API surface only. Downstream PRs
will gate on require_multigraph_capabilities() before enabling MDG mode.
Refs: Wave 1 MultiDiGraph implementation order.
* test: filter known third-party analyze warnings
---------
Co-authored-by: vampyre <vampyre@local.net>
- fix SQL extractor using bare path.stem as node ID prefix — collides across same-named files in different dirs; use _file_stem() (directory-qualified) instead
- fix Python import resolver keying stem_to_entities by bare stem; add bare_to_qualified secondary index for absolute imports so cross-file edges survive duplicate filenames
- add stat-based mtime fastpath to file_hash: skip full SHA256 when size+mtime_ns unchanged, flush index atomically via atexit (same trade-off as make)
- add cache-check, merge-chunks, merge-semantic CLI subcommands so the skill pipeline can use library functions instead of inline Python
- fix absolute source_file paths from semantic subagents not being relativized before graph storage (#932): add root param to build_from_json/build/build_merge, pass scan target at both call sites
- fix failed semantic chunks permanently freezing their files in the manifest (#933): filter _manifest_files to only include doc/paper/image files that appear in sem_result nodes/edges before calling save_manifest
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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>
When `root` has at least one direct symlinked child, default to following
symlinks instead of silently dropping their contents. This makes "fake
working dir" patterns (a folder full of symlinks pointing at scattered
source dirs) work transparently — the caller no longer has to know to
pass `follow_symlinks=True`.
Concrete motivating shape:
~/projects/research-corpus/
├── papers -> /external/drive/papers
├── notes -> /external/drive/notes
└── code -> /external/drive/code
Before: `--update` invoked `detect_incremental(root)` without passing
`follow_symlinks=True`, so the scan saw the small set of files actually
inside the root and missed everything reachable only through a symlink.
Result: every legitimate new file was missed, and the manifest paths
were marked as deleted.
After: when `follow_symlinks` is left at its default `None`, `detect()`
runs `_auto_follow_symlinks(root)` (one cheap `iterdir()` + `is_symlink()`
loop) and follows symlinks if any direct child is one. Behaviour is
unchanged for ordinary scans (no direct symlinks → False, as before).
Override is always possible by passing an explicit `follow_symlinks=True`
or `follow_symlinks=False`; existing tests confirming the explicit
behaviour continue to pass unchanged.
Backwards compatibility:
- Type annotation: `bool` -> `bool | None`. Callers passing `True`/`False`
continue to work identically. Callers passing nothing get the new
auto-detect.
- No new dependencies.
- Cheap: one `iterdir()` call once per detect() invocation.
Tests:
- 3 new tests in tests/test_detect.py:
- test_detect_auto_detects_direct_symlink_child
- test_detect_default_does_not_follow_when_no_symlinks
- test_detect_explicit_false_overrides_auto_detect
- Full tests/test_detect.py + tests/test_incremental.py: 49/49 pass.
#873: Remove blanket dot-prefix exclusion from detect.py and
extract.py collect_files(). Add framework caches (.next, .nuxt,
.turbo, .angular, .idea, .cache, .parcel-cache, .svelte-kit,
.terraform, .serverless, .graphify) to _SKIP_DIRS so they stay
blocked. Meaningful dot dirs (.github, .claude, etc.) are now
indexed.
#874: Add _maybe_reload() with mtime+size stat key and threading.Lock
to serve.py. call_tool and read_resource call _maybe_reload() on
every request; the graph reloads automatically when graph.json changes
without restarting the MCP server.
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>
`detect_incremental(root)` always called `detect(root)` without forwarding
the `follow_symlinks` kwarg. As a result, corpora that include symlinked
sub-trees pointing to directories outside the scan root (e.g. a
`state_of_truth/` symlink pointing at `~/.hermes/state_of_truth/`) were
visible to a full `detect()` run with `follow_symlinks=True` but invisible
to any subsequent `--update` run. The incremental scan would then either
report no changes (silently dropping legitimate new files) or repeatedly
re-extract a phantom subset, depending on what was reachable without
crossing symlinks.
Add a keyword-only `follow_symlinks` parameter to `detect_incremental()`
and forward it. Default stays `False` for backwards compatibility — only
callers that already opt in to symlink following on `detect()` pick up
the new behaviour for incremental runs too.
Test: a corpus with a symlinked directory is invisible with
`follow_symlinks=False`, fully indexed with `follow_symlinks=True`, and
correctly reports zero new files on a second incremental scan after the
manifest is saved.
safishamsi