fix: resolve P2 sync noise and cleanup issues

- bd-6pni: Auto-filter tombstoned issues with mismatched prefixes during
  import instead of failing. Tombstones from contributor PRs with different
  test prefixes are pollution and safe to ignore.

- bd-ffr9: Stop recreating deletions.jsonl after tombstone migration.
  Added IsTombstoneMigrationComplete() check to all code paths that write
  to the legacy deletions manifest.

- bd-admx: Fix perpetual "JSONL file hash mismatch" warning. Now clears
  both export_hashes AND jsonl_file_hash when mismatch detected, so the
  warning doesn't repeat.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

cmd/bd/doctor/fix/deletions.go

@@ -16,12 +16,21 @@ import (
 // HydrateDeletionsManifest populates deletions.jsonl from git history.
 // It finds all issue IDs that were ever in the JSONL but are no longer present,
 // and adds them to the deletions manifest.
+// Note (bd-ffr9): After tombstone migration, this is a no-op since inline tombstones
+// are used instead of deletions.jsonl.
 func HydrateDeletionsManifest(path string) error {
 	if err := validateBeadsWorkspace(path); err != nil {
 		return err
 	}
 
 	beadsDir := filepath.Join(path, ".beads")
+
+	// bd-ffr9: Skip hydrating deletions.jsonl if tombstone migration is complete
+	if deletions.IsTombstoneMigrationComplete(beadsDir) {
+		fmt.Println("  Tombstone migration complete - skipping deletions.jsonl hydration")
+		return nil
+	}
+
 	// bd-6xd: issues.jsonl is the canonical filename
 	jsonlPath := filepath.Join(beadsDir, "issues.jsonl")