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shazebandsafishamsi
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With `graphify extract --out <dir>`, the semantic cache write and read sides disagreed on both location and key anchoring, breaking the cache round-trip in two ways: - Checkpoints (#1990): `_checkpoint_chunk` called `save_semantic_cache` with only `root=target`, so per-chunk recovery checkpoints were written under `<corpus>/graphify-out/` while the reader consulted `<out>/graphify-out/` — creating an unwanted graphify-out/ inside the analyzed source tree and making every interrupted run re-extract (and re-bill) completed chunks. - Final save (#1991): cli.py passed `root=out_root`, so corpus-relative `source_file` paths resolved against the --out directory, failed `p.is_file()`, and every result group was silently skipped — the cache the reader would consult was never populated at all, with no warning. Fix, following the split the AST cache already uses (#1774): - `save_semantic_cache` and `check_semantic_cache` gain a `cache_root` parameter mirroring `load_cached`/`save_cached`: `root` stays the source-key anchor (content-hash keys, source_file resolution and relativization), `cache_root` selects where cache files live. Omitting it keeps `root` for both, so existing callers are unchanged. - `extract_corpus_parallel` plumbs `cache_root` into `_checkpoint_chunk`. - cli.py extract passes `root=target, cache_root=out_root` at the cache read, the checkpoint path, and the final save, and re-anchors the prune sweep's live hashes to `target` (keys anchored to out_root would mismatch every entry and sweep the fresh cache as orphaned). - `save_semantic_cache` now warns loudly when every result group is dropped because its source_file does not resolve to a real file — the silent-0-writes failure mode #1991 asked to surface. Regression tests cover: checkpoint written under cache_root (not the corpus, no corpus graphify-out/ created), recovery read finds the checkpoint via the same root/cache_root split, the final-save call shape writes entries where the reader looks, the all-groups-dropped warning, and backward compatibility when cache_root is omitted. Fixes #1990 Fixes #1991