fix(db): loop-append dense unresolved-ref result rows; make stripped-salvage visible (#1558) (#1576)

Real-world validation of #1575 on indexes damaged by the released v1.5.0
binary surfaced both of these.

getUnresolvedReferencesByFiles chunked its INPUT under SQLite's parameter
limit but appended each chunk's RESULT rows with a spread — every row
becomes a call argument, so a dense recovery sync (the #1541 self-heal
re-indexing 919 files produced 234,440 rows) exceeded V8's argument limit
and killed resolution mid-sync with "Maximum call stack size exceeded",
leaving the graph 226k edges short until another sync resumed the orphans
(and that sweep resolves measurably worse than the batched path — see the
follow-up issue). The failed-ref retry loader had the identical pattern on
unbounded result rows. Both append with a loop now (#1558).

The #1575 stripped-salvage warning also never rendered: init's summary
prints only index_partial warnings and counts only hard errors, so a run
with salvaged files still read as fully clean — and with no hard errors the
detail wasn't written to errors.log either. Salvage entries now carry code
'salvaged_stripped', the summary prints a visible warning naming the files,
and errors.log is written for salvage-only runs.

Validated on real corpora with full-graph dumps: healthy-path inits stay
byte-identical to the pre-#1575 baseline (cpython Lib, Alamofire, with a
determinism control); a realistically-damaged index (41 wiped + 5 missing
files, damage generated by the released binary) heals in one plain sync to
identical per-file counts and an edge set within the normal incremental
residual; pathological mass damage (52% of the repo) completes without
crashing. New regression test reproduces the RangeError on the old code
with 200k pending refs.

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>

CHANGELOG.md

@@ -49,6 +49,7 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 - The blast-radius section of `codegraph_explore` flagged "no covering tests found" whenever no test called a symbol directly — falsely branding helpers that tests exercise through their callers as untested (about 40% of flagged symbols in a measured sample). The check now follows caller chains up to 3 hops and reports indirect coverage as "tested via callers"; when nothing is found it states exactly what was checked instead of an unconditional warning. Thanks @inth3shadows for measuring the false-positive rate. (#1475)
 - Fixed a v1.5.0 regression where a perfectly valid file could be permanently recorded as having 0 symbols, with no error reported. When a file's first parse attempt was interrupted — a parsing worker crash or timeout, most likely on slow or heavily loaded machines — the automatic retry stored an empty result for any language on the native extraction path, so the file's functions and classes silently vanished from search, callers, and impact until the file was next edited. Retries now store the file's real symbols, and a file already recorded as symbol-free is detected and repaired automatically by the next sync or re-index after upgrading. Thanks @Baiae for the report. (#1541)
 - When indexing has to fall back to parsing a file with its comment lines stripped — a last-resort recovery after repeated parser crashes — the file is now flagged with a visible warning instead of being reported as cleanly indexed. The recovered result can be incomplete, and reporting success made a fresh index quietly disagree with a later re-parse of the same unchanged file. Thanks @jeremypetz for the precise init-versus-sync symbol accounting that exposed this. (#1565)
+- Syncing a large batch of changed files no longer crashes with "Maximum call stack size exceeded" partway through. The crash aborted reference resolution after the files' symbols were already stored, leaving the graph with far fewer connections than a fresh index would have — and it hit exactly the scenarios that re-parse many files at once, including the automatic repair above. Thanks @netbrah for pinpointing the failure. (#1558)
 
 ## [1.5.0] - 2026-07-21