Greptile Summary

This PR centralises all exclude-directory logic into a single src/constants/codebase-context.ts source of truth and converts the indexer's previously non-recursive glob patterns (coverage/**) to recursive ones (**/coverage/**), fixing index pollution from nested monorepo packages and worktree checkouts.

Changes:

• src/constants/codebase-context.ts — adds EXCLUDED_DIRECTORY_NAMES (readonly tuple), EXCLUDED_GLOB_PATTERNS (**/{dir}/** mapped from the tuple), and DISCOVERY_ONLY_IGNORED; this eliminates three separate hardcoded lists
• src/core/indexer.ts — drops the partial, non-recursive exclude list in favour of EXCLUDED_GLOB_PATTERNS; the key fix: coverage/** → **/coverage/** so deeply-nested generated artifacts are now excluded
• src/core/file-watcher.ts — adopts the shared patterns and gains previously-missing directories (build, target, vendor, .claude, worktrees)
• src/utils/project-discovery.ts — rebuilds IGNORED_DIRECTORY_NAMES from the two shared constants; backward-compatible, only adds new entries
• tests/indexer-exclude-patterns.test.ts — new integration test reproducing the exact audit failure; two minor issues: analyzerRegistry is not cleaned up in afterEach (potential singleton pollution if more tests are added), and the index-format fallback silently returns [] which could mask polluter-assertion failures

Issues found:

• EXCLUDED_GLOB_PATTERNS is typed as mutable string[] rather than readonly string[], allowing callers to accidentally mutate the shared constant
• analyzerRegistry.register in beforeEach has no corresponding cleanup, risking duplicate registrations across tests
• The index-format fallback in the test defaults to an empty array silently, which can make the polluter assertions trivially pass without actually testing anything
• [...EXCLUDED_GLOB_PATTERNS] spread in file-watcher.ts is a no-op copy of an already-mutable array

Confidence Score: 4/5

• Safe to merge — the core change is correct and well-tested; only minor style and test-robustness issues remain
• The logic change (making glob patterns recursive and centralising them) is straightforward and strictly improves coverage with no regressions. The existing consumers are all updated consistently and the behaviour for previously-excluded directories is unchanged. The one-point deduction reflects the two test issues (registry pollution and silent empty-chunk fallback) that could mask regressions in future iterations of the test suite.
• tests/indexer-exclude-patterns.test.ts — analyzerRegistry cleanup and silent fallback; src/constants/codebase-context.ts — EXCLUDED_GLOB_PATTERNS mutability

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A[src/constants/codebase-context.ts] -->|EXCLUDED_DIRECTORY_NAMES| B[EXCLUDED_GLOB_PATTERNS\n**\/dir\/**]
    A -->|DISCOVERY_ONLY_IGNORED| C[project-discovery\nIGNORED_DIRECTORY_NAMES]
    B --> D[src/core/indexer.ts\nexclude: EXCLUDED_GLOB_PATTERNS]
    B --> E[src/core/file-watcher.ts\nignored: EXCLUDED_GLOB_PATTERNS]
    A -->|EXCLUDED_DIRECTORY_NAMES| C

    D -->|glob exclude| F{File path\nmatches **/dir/**?}
    E -->|chokidar ignored| F
    C -->|Set.has check| G{Directory name\nin ignored set?}

    F -->|Yes| H[Skip — not indexed / not watched]
    F -->|No| I[Index / Watch]
    G -->|Yes| J[Skip — don't recurse]
    G -->|No| K[Recurse into directory]

_{Last reviewed commit: "style: format with p..."}