refactor: remove all deletions.jsonl code (bd-fom)

Complete removal of the legacy deletions.jsonl manifest system.
Tombstones are now the sole deletion mechanism.

Removed:
- internal/deletions/ - entire package
- cmd/bd/deleted.go - deleted command
- cmd/bd/doctor/fix/deletions.go - HydrateDeletionsManifest
- Tests for all removed functionality

Cleaned:
- cmd/bd/sync.go - removed sanitize, auto-compact
- cmd/bd/delete.go - removed dual-writes
- cmd/bd/doctor.go - removed checkDeletionsManifest
- internal/importer/importer.go - removed deletions checks
- internal/syncbranch/worktree.go - removed deletions merge
- cmd/bd/integrity.go - updated validation (warn-only on decrease)

Files removed: 12
Lines removed: ~7500

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

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

cmd/bd/doctor/fix/migrate.go

@@ -37,17 +37,6 @@ func DatabaseVersion(path string) error {
 			return fmt.Errorf("failed to initialize database: %w", err)
 		}
 
-		// bd-8v5o: Clean up deletions manifest for hydrated issues
-		// After init, remove any issues from deletions.jsonl that exist in JSONL
-		// This prevents perpetual "Skipping bd-xxx (in deletions manifest)" warnings
-		jsonlPath := findJSONLPath(beadsDir)
-		if jsonlPath != "" {
-			if err := cleanupDeletionsManifest(beadsDir, jsonlPath); err != nil {
-				// Non-fatal - just log warning
-				fmt.Printf("  Warning: failed to clean up deletions manifest: %v\n", err)
-			}
-		}
-
 		return nil
 	}