The atomic-write PR left several writers on the old truncate-then-write path.
Route them through write_json_atomic so a crash mid-write can't corrupt them:
- the --no-cluster raw graph.json dump (a core graph.json writer)
- merge-graphs / merge-chunks / merge-semantic output
- .graphify_analysis.json and .graphify_labels.json sidecars
- global_graph.py's global-graph.json and global-manifest.json
write_json_atomic gains an ensure_ascii flag so the raw-UTF-8 writers
(labels, merge outputs) keep byte-for-byte output. Adds tests for the
Windows PermissionError copy fallback and ensure_ascii=False.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
graph.json (the clustered `to_json` write and the `--no-cluster`/merge raw
dumps) and manifest.json were written with a direct `open()`/`write_text`, so a
crash, kill, or disk-full mid-write left a truncated, unparseable file that the
next load or `detect_incremental` then failed on.
Add `write_text_atomic`/`write_json_atomic` in graphify.paths (temp file in the
same directory + `os.replace`; JSON is streamed into the temp, not materialized
as one string) and route the graph.json writers (export.to_json,
cli._prune_graph_json_sources, the merge driver) plus detect.save_manifest
through them. The helper preserves the destination's mode (an atomic replace
never tightens 0644 to mkstemp's 0600), writes through a symlinked destination
(shared-output setups), and falls back to copy-then-delete on a Windows
os.replace lock — matching graphify.cache's existing atomic writer. On failure
the previous file is left intact and the temp removed. Not a power-loss
durability guarantee (no fsync, consistent with the rest of the codebase).
The cross-file call resolver bailed (#543/#1219 god-node guard) whenever a
bare callee name had 2+ definitions without unique import evidence — so a
single same-named test mock (or any same-named symbol) dropped the real
`calls` edge, erasing the call graph wherever a mock existed (the reporter
saw a 76-stub Pester suite wipe everything).
Replace the blunt bail with a smarter guard: when a name is ambiguous and
import evidence doesn't resolve it, apply tie-breakers — non-test
preference (a shared, segment-aware _is_test_path classifier) then path
proximity — and emit an INFERRED edge ONLY if exactly one candidate
survives, else keep bailing. A real def + a test mock resolves to the real
def; two genuine non-test defs still bail (god-node guard intact, no
fan-out). Wired into both the extract.py pass and the symbol_resolution.py
copy via the shared classifier.
Reported by @Schweinehund.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The GRAPHIFY_OUT override (custom output-dir name / absolute path, #686) was only
respected by some readers. `graphify extract` and several commands hardcoded the
literal "graphify-out", so `GRAPHIFY_OUT=custom-out graphify extract` still wrote
to graphify-out/ and downstream query/serve/update looked in the wrong place.
Resolve the output-dir name through graphify.paths everywhere it matters:
- new graphify.paths.out_path()/default_graph_json() helpers
- __main__: extract write dir, cluster-only/label, query/affected/benchmark
defaults, save-result --memory-dir, uninstall --purge, cache-check
- detect: _MANIFEST_PATH, memory/ + converted/ dirs, and the scan-exclude (a
renamed output dir is no longer re-ingested as source input)
- transcribe._TRANSCRIPTS_DIR; build_merge/serve/benchmark/prs graph-path defaults
Default behaviour is unchanged: with no env var everything still uses graphify-out/.
Verified end-to-end (extract -> cluster-only -> query under GRAPHIFY_OUT=custom-out
writes/reads custom-out/, no stray graphify-out/) and added a CLI regression test.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
#1418: build_from_json relativized source_file on nodes and edges but stored
graph.hyperedges[] verbatim, so a semantic subagent's absolute path leaked into
graph.json. Relativize hyperedges in build_from_json (to_json has no root to
relativize against), mirroring the existing node/edge handling.
#1423: consolidate the GRAPHIFY_OUT output-dir name into a single graphify.paths
module (was duplicated in __main__, cache, watch) and route the path guards
through it — security.validate_graph_path's base=None discovery + fallback,
callflow_html's project-root resolution, and the post-commit/post-checkout hook
bodies (which now read the env var at hook-run time). A renamed output dir is no
longer validated against the wrong base or missed by the hook.
Tests: hyperedge relativization (test_hypergraph), GRAPHIFY_OUT discovery
(test_security), updated the hook-body contract assertion (test_hooks).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
safishamsi