fix(extraction): decode kernel results in indexAll retry passes; self-heal wiped rows (#1541) (#1575)

The parse-pool workers return kernel-language extractions as an undecoded
buffer transport (nodes/edges EMPTY, tables in kernelBuffers). indexAll's
main loop decodes them (or hands the buffers to the store worker), but its
two retry passes — plain retry and the comments-stripped last resort —
stored the transport as-is: the storage gate passed via errors.length === 0,
zero nodes were inserted, and the files row was written with node_count = 0
while the original error was spliced out of the summary. Any worker
crash/timeout whose in-flight file was a kernel-routed language permanently
recorded that file as "(0 symbols)" — silently, and immune to later syncs
because the stored hash matches the on-disk bytes (#1541; v1.4.1 predates
the kernel path, which is why it was unaffected).

- Both retry passes now materialize kernel results before the gate, store,
  counters, and log lines.
- storeExtractionResult materializes at entry as defense-in-depth, so no
  storage path can persist an undecoded transport again.
- Zero-node rows on symbol-bearing languages (only the wipe produces these —
  every real extraction stores at least the file node) are dropped during
  full-reconcile sync and indexAll so already-affected files re-index
  automatically after upgrading. Scoped watcher syncs leave rows outside
  their scope untouched.
- The comments-stripped salvage now downgrades the failure to a visible
  warning instead of erasing it: the recovered result can be incomplete, and
  reporting clean success made a fresh index quietly disagree with a later
  per-file re-parse of the same bytes (#1565's init-vs-sync divergence).

Repro (released 1.5.0): CODEGRAPH_PARSE_TIMEOUT_MS=1 codegraph init on any
Python project → "Retry OK: <file> (0 nodes)" and permanent
"(python, 0 symbols)" rows. Fixed build stores real symbols under the same
forcing, and heals rows wiped by prior runs.

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

CHANGELOG.md

@@ -47,6 +47,8 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 - When a `codegraph_explore` answer shows a file as excerpts, a large excerpt that no longer fit was dropped entirely instead of being shortened. If the file's first excerpt happened to be a trivial one — an import block, a one-line helper next to the code you asked about — the excerpt carrying the actual answer was the one thrown away, and the file came back with a quarter of the room it had been given. On real projects that meant the top-ranked file delivered a fraction of its share while a far less relevant file took the rest. Excerpts are now shortened to fit, whole method by whole method, and only dropped when what is left is too small to hold anything readable.
 - When you name a symbol in a `codegraph_explore` query, its definition now actually comes back. Two cases previously lost it. If the symbols you named don't call one another — sibling functions inside the same factory or module are the everyday example — CodeGraph stopped treating them as symbols you had asked for, and answered with whatever sat at the top of their file instead; on one 1,400-line file that meant a same-stem `QueuedMessage` interface on line 70 came back while the `queueMessage` function on line 1087 did not. And when an answer had to be trimmed to fit, it was trimmed from the bottom of the file down, so a symbol near the end of a long file was always the first thing cut. Trimming now protects the definitions you named wherever they sit in the file.
 - 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)
 
 ## [1.5.0] - 2026-07-21