Adds support for Quarto markdown (.qmd) files by:
- Adding '.qmd' to document file extensions in detection
- Updating export logic to handle .qmd in filename sanitization
- Adding .qmd extractor dispatch using the existing markdown extractor
- Updating watch comments to include .qmd files
The cross-file call resolver in `extract()` unconditionally marked every
resolved call edge as INFERRED with confidence_score 0.8 — even when the
caller's file had an explicit `imports` (symbol) or `imports_from`
(module) edge to the callee. The new CJS require handler made this gap
visible: imports were correctly EXTRACTED but the call edges that those
imports backed remained INFERRED, so downstream consumers couldn't tell
high-evidence calls apart from name-match guesses.
This pass runs after the file-id remap (line 4736), so we relativize
node `source_file` paths before computing file_nids — otherwise the
caller's computed file_nid (absolute-path-derived) wouldn't match the
imports_from edge source (already remapped to relative form).
Promotion rule:
- Symbol-level `imports` edge from caller's file -> callee node id
=> EXTRACTED, confidence_score 1.0
- Module-level `imports_from` edge from caller's file -> callee's file
=> EXTRACTED, confidence_score 1.0
- Otherwise => INFERRED, confidence_score 0.8 (existing behavior)
Validated on a 92-file CJS orchestrator: 5 previously-INFERRED edges
from runExecute() now resolve to EXTRACTED, and 88% of cross-file calls
in the corpus (104 of 118) promote, leaving INFERRED only for genuine
heuristic guesses with no import backing.
Adds two tests:
- test_cross_file_call_promoted_to_extracted_with_import_evidence
- test_cross_file_call_remains_inferred_without_import_evidence
The JS/TS extractor only handled ES `import` statements; CommonJS
`require()` calls produced no import edges. Downstream, the call-graph
pass could not resolve which symbols belonged to which file, so every
cross-file call in CJS Node.js codebases was downgraded to INFERRED
even when the binding was a top-of-file destructured require.
Adds three patterns to `_js_extra_walk` via a new `_require_imports_js`
helper:
const { foo, bar: alias } = require('./mod') -> imports_from + per-symbol imports
const mod = require('./mod') -> imports_from
const x = require('./mod').y -> imports_from + symbol edge for y
Refactors path-resolution out of `_import_js` into
`_resolve_js_import_target` so ES imports and CJS requires share the
relative / tsconfig-alias / bare-module logic.
Tested in a 92-file CJS Node.js orchestrator codebase: confirmed all
five previously INFERRED `runExecute -> {loadFoundation,
validateDispatchConfig, fetchSymphonyIssues, listSymphonyWorktrees,
workspacePathForIssue}` edges resolve to real top-of-file destructured
requires, so downstream calls would now be EXTRACTED instead of
INFERRED.
Add `.luau` to CODE_EXTENSIONS and route it through extract_lua
(tree-sitter-lua). Roblox first-party code uses .luau; without this,
graphify silently skipped 379/479 files on a real Roblox codebase
and the resulting graph was dominated by vendored .lua dependencies.
tree-sitter-lua doesn't parse Luau type annotations, but it
successfully extracts function declarations and call edges from
Luau source — verified on a 379-file Roblox codebase (1265 nodes,
1471 edges, 236 communities).
A dedicated tree-sitter-luau grammar would be a richer long-term
fix; this is the minimal change to make Luau projects work today.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
The initial Gemini backend defaulted to 2.5 Flash, but large semantic extraction chunks can benefit from newer models and more output headroom. Move the default to Gemini 3 Flash Preview, add CLI and environment model overrides, and increase the Gemini completion budget while keeping low reasoning effort for cost control.
Constraint: Google exposes Gemini through an OpenAI-compatible chat-completions endpoint
Rejected: Hardcode Gemini 3.1 Pro as the default | higher cost for routine repository indexing
Confidence: medium
Scope-risk: narrow
Directive: Keep --model and GRAPHIFY_GEMINI_MODEL working before changing Gemini defaults again
Tested: uv run --directory vendor/graphify pytest tests/test_llm_backends.py tests/test_chunking.py -q
Not-tested: Live Gemini 3 extraction on the full cloud-edge repo before this commit
`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.
Gemini is often the cheaper available quota for low-stakes semantic graph extraction, while OpenAI is a useful fallback. Extend the direct extraction backend registry, CLI validation, docs, and tests so headless extraction can use GEMINI_API_KEY, GOOGLE_API_KEY, or OPENAI_API_KEY without changing the existing Claude and Kimi paths.
Constraint: Gemini supports OpenAI-compatible chat completions at the Google generative-language endpoint
Rejected: Native google-genai integration | higher dependency and response-shape churn for the same chat-completions path
Confidence: medium
Scope-risk: moderate
Directive: Keep backend detection explicit and test every accepted API-key environment variable before adding new providers
Tested: uv run --directory vendor/graphify pytest tests/test_llm_backends.py tests/test_chunking.py -q
Not-tested: Live Gemini/OpenAI API calls; no GEMINI_API_KEY or OPENAI_API_KEY present in this environment
- Register .groovy and .gradle in CODE_EXTENSIONS, _DISPATCH, and collect_files
- Add _GROOVY_CONFIG (reuses Java import handler)
- Add regex-based _extract_spock_fallback for Spock spec files where
tree-sitter-groovy wraps the body in ERROR nodes due to def-string methods
- _is_spock_file detects via regex scan (def "...") instead of node-label
heuristic, avoiding false negatives on classes whose name differs from stem
- Fallback retains only file node + import edges from tree-sitter pass to
prevent orphaned constructor/method nodes
- Add tree-sitter-groovy>=0.1.2 dependency
- Add 11 tests covering plain Groovy and Spock paths, including apostrophe
in feature method names
Safi