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/import.go

@@ -96,8 +96,6 @@ NOTE: Import requires direct database access and does not work with daemon mode.
 		clearDuplicateExternalRefs, _ := cmd.Flags().GetBool("clear-duplicate-external-refs")
 		orphanHandling, _ := cmd.Flags().GetString("orphan-handling")
 		force, _ := cmd.Flags().GetBool("force")
-		noGitHistory, _ := cmd.Flags().GetBool("no-git-history")
-		ignoreDeletions, _ := cmd.Flags().GetBool("ignore-deletions")
 		protectLeftSnapshot, _ := cmd.Flags().GetBool("protect-left-snapshot")
 
 		// Check if stdin is being used interactively (not piped)
@@ -257,8 +255,6 @@ NOTE: Import requires direct database access and does not work with daemon mode.
 			RenameOnImport:             renameOnImport,
 			ClearDuplicateExternalRefs: clearDuplicateExternalRefs,
 			OrphanHandling:             orphanHandling,
-			NoGitHistory:               noGitHistory,
-			IgnoreDeletions:            ignoreDeletions,
 		}
 
 		// If --protect-left-snapshot is set, read the left snapshot and build ID set
@@ -423,18 +419,8 @@ NOTE: Import requires direct database access and does not work with daemon mode.
 		if len(result.IDMapping) > 0 {
 			fmt.Fprintf(os.Stderr, ", %d issues remapped", len(result.IDMapping))
 		}
-		if result.SkippedDeleted > 0 {
-			fmt.Fprintf(os.Stderr, ", %d skipped (deleted)", result.SkippedDeleted)
-		}
 		fmt.Fprintf(os.Stderr, "\n")
 
-		// Print skipped deleted issues summary if any (bd-4zy)
-		if result.SkippedDeleted > 0 {
-			fmt.Fprintf(os.Stderr, "\n⚠️  Skipped %d issue(s) found in deletions manifest\n", result.SkippedDeleted)
-			fmt.Fprintf(os.Stderr, "   These issues were previously deleted and will not be resurrected.\n")
-			fmt.Fprintf(os.Stderr, "   Use --ignore-deletions to force import anyway.\n")
-		}
-
 		// Print skipped dependencies summary if any
 		if len(result.SkippedDependencies) > 0 {
 			fmt.Fprintf(os.Stderr, "\n⚠️  Warning: Skipped %d dependencies due to missing references:\n", len(result.SkippedDependencies))
@@ -790,8 +776,6 @@ func init() {
 	importCmd.Flags().Bool("clear-duplicate-external-refs", false, "Clear duplicate external_ref values (keeps first occurrence)")
 	importCmd.Flags().String("orphan-handling", "", "How to handle missing parent issues: strict/resurrect/skip/allow (default: use config or 'allow')")
 	importCmd.Flags().Bool("force", false, "Force metadata update even when database is already in sync with JSONL")
-	importCmd.Flags().Bool("no-git-history", false, "Skip git history backfill for deletions (use during JSONL filename migrations)")
-	importCmd.Flags().Bool("ignore-deletions", false, "Import issues even if they're in the deletions manifest")
 	importCmd.Flags().Bool("protect-left-snapshot", false, "Protect issues in left snapshot from git-history-backfill (bd-sync-deletion fix)")
 	importCmd.Flags().BoolVar(&jsonOutput, "json", false, "Output import statistics in JSON format")
 	rootCmd.AddCommand(importCmd)