fix: honor exclude globs so matched files are omitted from the index

[lisarium]

Summary

Config exclude globs were recorded as skipped but still indexed, because walkDirectory continued only the inner pattern loop. Matching files (and stale failed-batch retries for those paths) are now omitted from the index.

Changes

• Skip files as soon as an exclude glob matches in collectFiles / walkDirectory, instead of falling through to include matching.
• Skip walking directories covered by /** exclude globs (for example **/common/**).
• Drop stale failed-batch retries for newly excluded paths on incremental /index and retryFailedBatches.
• Document the behavior and add unit/indexer coverage.

Testing

How were these changes tested?

• Unit tests added/updated
• Manual testing performed
• Build passes (npm run build)
• Typecheck passes (npm run typecheck)
• Tests pass (npm run test:run)
• Lint passes (npm run lint)

Release Labels

• Added at least one release category label (feature, bug, performance, documentation, dependencies, refactor, test, chore, or skip-changelog)
• Added at most one semver label (semver:major, semver:minor, or semver:patch) when needed

Labels: bug

Related Issues

No tracked issue.

[lisarium]

@Helweg Hi, could you please approve the first-time-contributor workflows and add bug label to this PR?

[Helweg]

Review finding

isStoredPathExcluded() now checks the absolute storedPath against config globs before normalizing project-owned paths relative to the project (src/indexer/index.ts:1268-1271). In global scope, the default **/.*/** can match a hidden parent directory such as /Users/me/.work/project, so valid failed batches are silently discarded instead of retried.

Please normalize project-owned absolute paths before glob matching, then add coverage for a project beneath a hidden directory. I verified the regression: the PR fails 5 affected failed-batch cases, while main passes 28/28 in the same setup. Build, CLI smoke test, native build, typecheck, and lint pass.