Case 1 — `extract <corpus> --out <dir>`: the graph went to <dir> (cache_root is
already passed to the AST extractor), but detect()'s word-count/stat-index cache
uses the scan root, so a stray graphify-out/cache/ was created inside the corpus
(and left behind even when the run aborted at the no-LLM-key gate). Thread an
optional cache_root through detect() -> cached_word_count() -> _ensure_stat_index()
and pass out_root from the extract CLI, so the stat index lives under --out. Entry
keys are absolute paths, so relocating the index file is safe.
Case 2 — `cluster-only --graph <elsewhere>/graphify-out/graph.json`: outputs
(GRAPH_REPORT.md, re-clustered graph.json, labels, analysis, html) were written to
the CWD's graphify-out/, ignoring where --graph lives. They now write beside the
input graph when it sits in a graphify-out/ dir (another project/tenant's output),
while still falling back to the CWD for an arbitrary archived backup/graph.json —
the restore-into-place workflow #934 pins.
Regression tests for both cases; #934 still passes.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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