fix: clear stale deleted-export advisories on full builds, not just incremental

[carlos-alm]

Summary

#1938 fixed deleted_export_advisories persistence for the incremental rebuild path (handleIncrementalBuild/clearDeletedExportAdvisories), but the full-build path (handleFullBuild / Rust's save_and_purge_changed full-build branch) never called the equivalent clear, so a full rebuild after a delete-then-recreate cycle could leave stale advisory rows behind, causing codegraph check to report a false-positive removed-export warning that a full build should have cleared.

This fix recovered from an orphaned worktree (found during /housekeep) — the work was done, verified, and never turned into a PR. Independently re-verified before landing: confirmed not superseded by any later independent fix, confirmed clean merge onto current origin/main (zero conflicts), and re-ran the full relevant test suite (both engines) from a fresh branch.

Verification

• npx vitest run tests/integration/check.test.ts tests/integration/issue-1938-deleted-export-advisory-persistence.test.ts: 68/68 pass (wasm + native)
• cargo test --release (codegraph-core): 753/753 pass
• npm run lint: clean
• codegraph diff-impact origin/main -T: 1 function changed (handleFullBuild), 3 transitive callers, 2 files — scoped as expected

Closes #2232

[greptile-apps]

Greptile Summary

The PR brings full-build handling of deleted-export advisories into parity with incremental builds, preventing stale removed-export warnings after a deleted file reappears.

• Clears advisory rows for every currently existing file reparsed by the TypeScript full-build path.
• Mirrors the cleanup in the Rust native pipeline.
• Adds native/WASM integration coverage for the delete, recreate, and full-rebuild lifecycle.
• Adds explicit types to the advisory test helper.

Confidence Score: 5/5

The PR appears safe to merge, with the TypeScript and Rust full-build paths consistently clearing stale advisories and regression coverage exercising both engines.

The cleanup targets currently existing full-build paths, safely handles empty and large path collections, and preserves advisories associated with files that remain deleted.

Important Files Changed

Filename	Overview
crates/codegraph-core/src/domain/graph/builder/pipeline.rs	Mirrors advisory cleanup in the Rust full-build branch using relative paths from the complete full-build change set.
src/domain/graph/builder/stages/detect-changes.ts	Clears stale advisory rows for all files included in a TypeScript full rebuild, with normalized relative-path fallback.
tests/integration/issue-1938-deleted-export-advisory-persistence.test.ts	Adds regression coverage proving a full rebuild clears the stale advisory after a deleted file reappears without exports.
tests/integration/check.test.ts	Adds concrete TypeScript annotations to the advisory insertion test helper without changing behavior.

Sequence Diagram

sequenceDiagram
  participant FS as Source files
  participant Build as Full-build pipeline
  participant DB as Graph database
  participant Check as codegraph check
  FS->>Build: Reappeared file is collected
  Build->>DB: Purge graph data
  Build->>DB: Clear stale advisories for parsed paths
  Build->>DB: Insert freshly parsed graph
  Check->>DB: Read current advisory state
  DB-->>Check: No stale removed-export warning

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[github-actions]

Codegraph Impact Analysis

1 functions changed → 3 callers affected across 2 files

• handleFullBuild in src/domain/graph/builder/stages/detect-changes.ts:631 (3 transitive callers)