fix #261, #249, #266 and bump to 0.4.4

- watch.py: preserve INFERRED/AMBIGUOUS edges (code<->doc) across rebuilds (#261)
- __main__.py: fix Codex hook - use additionalContext instead of permissionDecision:allow (#249)
- detect.py: skip common lockfiles (package-lock.json, yarn.lock, Cargo.lock etc.) (#266)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

CHANGELOG.md

@@ -2,6 +2,12 @@
 
 Full release notes with details on each version: [GitHub Releases](https://github.com/safishamsi/graphify/releases)
 
+## 0.4.4 (2026-04-12)
+
+- Fix: `watch` now preserves INFERRED/AMBIGUOUS edges (code↔doc rationale links) across rebuilds — previously all cross-type edges were dropped (#261)
+- Fix: Codex hook no longer emits `permissionDecision:allow` which codex-cli 0.120.0 rejects (#249)
+- Fix: Common lockfiles (`package-lock.json`, `yarn.lock`, `Cargo.lock`, etc.) are now skipped during detection, preventing token drain on large JS/Rust/Python projects (#266)
+
 ## 0.4.3 (2026-04-12)
 
 - Fix: JS/TS relative imports now resolve to full-path node IDs — previously all `imports_from` edges were silently dropped on large TypeScript codebases (#256)

graphify/__main__.py

@@ -428,7 +428,7 @@ _CODEX_HOOK = {
                         "type": "command",
                         "command": (
                             "[ -f graphify-out/graph.json ] && "
-                            r"""echo '{"hookSpecificOutput":{"hookEventName":"PreToolUse","permissionDecision":"allow"},"systemMessage":"graphify: Knowledge graph exists. Read graphify-out/GRAPH_REPORT.md for god nodes and community structure before searching raw files."}' """
+                            r"""echo '{"hookSpecificOutput":{"hookEventName":"PreToolUse","additionalContext":"graphify: Knowledge graph exists. Read graphify-out/GRAPH_REPORT.md for god nodes and community structure before searching raw files."}}' """
                             "|| true"
                         ),
                     }

graphify/detect.py

@@ -241,6 +241,13 @@ _SKIP_DIRS = {
     ".tox", ".eggs", "*.egg-info",
 }
 
+# Large generated files that are never useful to extract
+_SKIP_FILES = {
+    "package-lock.json", "yarn.lock", "pnpm-lock.yaml",
+    "Cargo.lock", "poetry.lock", "Gemfile.lock",
+    "composer.lock", "go.sum", "go.work.sum",
+}
+
 def _is_noise_dir(part: str) -> bool:
     """Return True if this directory name looks like a venv, cache, or dep dir."""
     if part in _SKIP_DIRS:
@@ -357,6 +364,8 @@ def detect(root: Path, *, follow_symlinks: bool = False) -> dict:
                     and not _is_ignored(dp / d, root, ignore_patterns)
                 ]
             for fname in filenames:
+                if fname in _SKIP_FILES:
+                    continue
                 p = dp / fname
                 if p not in seen:
                     seen.add(p)

graphify/watch.py

@@ -44,7 +44,8 @@ def _rebuild_code(watch_path: Path, *, follow_symlinks: bool = False) -> bool:
                 code_ids = {n["id"] for n in existing.get("nodes", []) if n.get("file_type") == "code"}
                 sem_nodes = [n for n in existing.get("nodes", []) if n.get("file_type") != "code"]
                 sem_edges = [e for e in existing.get("edges", [])
-                             if e.get("source") not in code_ids and e.get("target") not in code_ids]
+                             if e.get("confidence") in ("INFERRED", "AMBIGUOUS")
+                             or (e.get("source") not in code_ids and e.get("target") not in code_ids)]
                 result = {
                     "nodes": result["nodes"] + sem_nodes,
                     "edges": result["edges"] + sem_edges,

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "graphifyy"
-version = "0.4.3"
+version = "0.4.4"
 description = "AI coding assistant skill (Claude Code, Codex, OpenCode, Cursor, OpenClaw, Factory Droid, Trae) - turn any folder of code, docs, papers, images, or videos into a queryable knowledge graph"
 readme = "README.md"
 license = { file = "LICENSE" }