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>

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