fix(import): add warning when issues are skipped due to deletions manifest

When importing JSONL that contains issues in the deletions manifest,
import now:
- Filters out deleted issues before import
- Prints per-issue warning with deletion details (date, actor)
- Shows count of skipped issues in summary
- Suggests --ignore-deletions flag to force import

The new --ignore-deletions flag allows importing issues that are in the
deletions manifest, useful for recovering accidentally deleted issues.

Fixes bd-4zy

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

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

.beads/issues.jsonl

@@ -0,0 +1 @@
+{"id":"bd-4zy","title":"Import silently skips issues in deletions manifest","description":"**Problem**: When JSONL has valid issues but the deletions manifest lists them as deleted, bd import returns '0 created, 0 updated' with NO warning. This is confusing because issues exist in JSONL but aren't imported.\n\n**Expected behavior**: \n- At minimum: warn that N issues were skipped due to deletions manifest\n- Better: offer to restore them or show what's being skipped\n\n**Requirements**:\n1. Add warning message when issues are skipped due to deletions\n2. Show count and optionally list IDs of skipped issues\n3. Consider --force flag to import anyway (ignoring deletions)\n\n**Files to check**: cmd/bd/import.go, internal/importer/","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-30T21:14:47.146103-08:00","updated_at":"2025-11-30T21:21:33.428328-08:00","closed_at":"2025-11-30T21:21:33.428328-08:00","close_reason":"Implemented filtering of deleted issues during import with warning message and --ignore-deletions flag"}

cmd/bd/import.go

@@ -96,6 +96,7 @@ NOTE: Import requires direct database access and does not work with daemon mode.
 		orphanHandling, _ := cmd.Flags().GetString("orphan-handling")
 		force, _ := cmd.Flags().GetBool("force")
 		noGitHistory, _ := cmd.Flags().GetBool("no-git-history")
+		ignoreDeletions, _ := cmd.Flags().GetBool("ignore-deletions")
 
 		// Check if stdin is being used interactively (not piped)
 		if input == "" && term.IsTerminal(int(os.Stdin.Fd())) {
@@ -255,6 +256,7 @@ NOTE: Import requires direct database access and does not work with daemon mode.
 			ClearDuplicateExternalRefs: clearDuplicateExternalRefs,
 			OrphanHandling:             orphanHandling,
 			NoGitHistory:               noGitHistory,
+			IgnoreDeletions:            ignoreDeletions,
 		}
 
 		result, err := importIssuesCore(ctx, dbPath, store, allIssues, opts)
@@ -402,8 +404,18 @@ 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))
@@ -759,6 +771,7 @@ func init() {
 	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().BoolVar(&jsonOutput, "json", false, "Output import statistics in JSON format")
 	rootCmd.AddCommand(importCmd)
 }

cmd/bd/import_shared.go

@@ -166,6 +166,7 @@ type ImportOptions struct {
 	ClearDuplicateExternalRefs bool   // Clear duplicate external_ref values instead of erroring
 	OrphanHandling             string // Orphan handling mode: strict/resurrect/skip/allow (empty = use config)
 	NoGitHistory               bool   // Skip git history backfill for deletions (prevents spurious deletion during JSONL migrations)
+	IgnoreDeletions            bool   // Import issues even if they're in the deletions manifest
 }
 
 // ImportResult contains statistics about the import operation
@@ -183,6 +184,8 @@ type ImportResult struct {
 	SkippedDependencies []string          // Dependencies skipped due to FK constraint violations
 	Purged              int               // Issues purged from DB (found in deletions manifest)
 	PurgedIDs           []string          // IDs that were purged
+	SkippedDeleted      int               // Issues skipped because they're in deletions manifest
+	SkippedDeletedIDs   []string          // IDs that were skipped due to deletions manifest
 }
 
 // importIssuesCore handles the core import logic used by both manual and auto-import.
@@ -223,6 +226,7 @@ func importIssuesCore(ctx context.Context, dbPath string, store storage.Storage,
 		ClearDuplicateExternalRefs: opts.ClearDuplicateExternalRefs,
 		OrphanHandling:             importer.OrphanHandling(orphanHandling),
 		NoGitHistory:               opts.NoGitHistory,
+		IgnoreDeletions:            opts.IgnoreDeletions,
 	}
 
 	// Delegate to the importer package
@@ -246,6 +250,8 @@ func importIssuesCore(ctx context.Context, dbPath string, store storage.Storage,
 		SkippedDependencies: result.SkippedDependencies,
 		Purged:              result.Purged,
 		PurgedIDs:           result.PurgedIDs,
+		SkippedDeleted:      result.SkippedDeleted,
+		SkippedDeletedIDs:   result.SkippedDeletedIDs,
 	}, nil
 }
 

internal/importer/importer.go

@@ -43,6 +43,7 @@ type Options struct {
 	OrphanHandling             OrphanHandling // How to handle missing parent issues (default: allow)
 	ClearDuplicateExternalRefs bool           // Clear duplicate external_ref values instead of erroring
 	NoGitHistory               bool           // Skip git history backfill for deletions (prevents spurious deletion during JSONL migrations)
+	IgnoreDeletions            bool           // Import issues even if they're in the deletions manifest
 }
 
 // Result contains statistics about the import operation
@@ -60,6 +61,8 @@ type Result struct {
 	SkippedDependencies []string          // Dependencies skipped due to FK constraint violations
 	Purged              int               // Issues purged from DB (found in deletions manifest)
 	PurgedIDs           []string          // IDs that were purged
+	SkippedDeleted      int               // Issues skipped because they're in deletions manifest
+	SkippedDeletedIDs   []string          // IDs that were skipped due to deletions manifest
 }
 
 // ImportIssues handles the core import logic used by both manual and auto-import.
@@ -114,6 +117,29 @@ func ImportIssues(ctx context.Context, dbPath string, store storage.Storage, iss
 		opts.OrphanHandling = sqliteStore.GetOrphanHandling(ctx)
 	}
 
+	// Filter out issues that are in the deletions manifest (bd-4zy)
+	// Unless IgnoreDeletions is set, skip importing deleted issues
+	if !opts.IgnoreDeletions && dbPath != "" {
+		beadsDir := filepath.Dir(dbPath)
+		deletionsPath := deletions.DefaultPath(beadsDir)
+		loadResult, err := deletions.LoadDeletions(deletionsPath)
+		if err == nil && len(loadResult.Records) > 0 {
+			var filteredIssues []*types.Issue
+			for _, issue := range issues {
+				if del, found := loadResult.Records[issue.ID]; found {
+					// Issue is in deletions manifest - skip it
+					result.SkippedDeleted++
+					result.SkippedDeletedIDs = append(result.SkippedDeletedIDs, issue.ID)
+					fmt.Fprintf(os.Stderr, "Skipping %s (in deletions manifest: deleted %s by %s)\n",
+						issue.ID, del.Timestamp.Format("2006-01-02"), del.Actor)
+				} else {
+					filteredIssues = append(filteredIssues, issue)
+				}
+			}
+			issues = filteredIssues
+		}
+	}
+
 	// Check and handle prefix mismatches
 	if err := handlePrefixMismatch(ctx, sqliteStore, issues, opts, result); err != nil {
 		return result, err