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#1990Fixes#1991
