feat: Add bd init --from-jsonl for preserving manual cleanups

Adds --from-jsonl flag that imports from the current working tree's
.beads/issues.jsonl file instead of scanning git history. This prevents
deleted issues from being resurrected during re-initialization.

Use case: After running bd compact --purge-tombstones and committing
the cleaned JSONL, a subsequent bd init would previously re-import
all historical issues from git, defeating the cleanup.

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

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

cmd/bd/autoimport.go

@@ -206,6 +206,69 @@ func getLocalSyncBranch(beadsDir string) string {
 
 
 
+// importFromLocalJSONL imports issues from a local JSONL file on disk.
+// Unlike importFromGit, this reads from the current working tree, preserving
+// any manual cleanup done to the JSONL file (e.g., via bd compact --purge-tombstones).
+// Returns the number of issues imported and any error.
+func importFromLocalJSONL(ctx context.Context, dbFilePath string, store storage.Storage, localPath string) (int, error) {
+	// #nosec G304 -- path provided by bd init command
+	jsonlData, err := os.ReadFile(localPath)
+	if err != nil {
+		return 0, fmt.Errorf("failed to read local JSONL file: %w", err)
+	}
+
+	// Parse JSONL data
+	scanner := bufio.NewScanner(bytes.NewReader(jsonlData))
+	// Increase buffer size to handle large JSONL lines (e.g., big descriptions)
+	scanner.Buffer(make([]byte, 0, 1024*1024), 64*1024*1024) // allow up to 64MB per line
+	var issues []*types.Issue
+
+	for scanner.Scan() {
+		line := scanner.Text()
+		if line == "" {
+			continue
+		}
+
+		var issue types.Issue
+		if err := json.Unmarshal([]byte(line), &issue); err != nil {
+			return 0, fmt.Errorf("failed to parse issue: %w", err)
+		}
+		issue.SetDefaults() // Apply defaults for omitted fields
+		issues = append(issues, &issue)
+	}
+
+	if err := scanner.Err(); err != nil {
+		return 0, fmt.Errorf("failed to scan JSONL: %w", err)
+	}
+
+	// Set issue_prefix from first imported issue if missing
+	if len(issues) > 0 {
+		configuredPrefix, err := store.GetConfig(ctx, "issue_prefix")
+		if err == nil && strings.TrimSpace(configuredPrefix) == "" {
+			firstPrefix := utils.ExtractIssuePrefix(issues[0].ID)
+			if firstPrefix != "" {
+				if err := store.SetConfig(ctx, "issue_prefix", firstPrefix); err != nil {
+					return 0, fmt.Errorf("failed to set issue_prefix from imported issues: %w", err)
+				}
+			}
+		}
+	}
+
+	// Use existing import logic
+	opts := ImportOptions{
+		DryRun:               false,
+		SkipUpdate:           false,
+		SkipPrefixValidation: true,
+	}
+
+	_, err = importIssuesCore(ctx, dbFilePath, store, issues, opts)
+	if err != nil {
+		return 0, err
+	}
+
+	return len(issues), nil
+}
+
 // importFromGit imports issues from git at the specified ref (bd-0is: supports sync-branch)
 func importFromGit(ctx context.Context, dbFilePath string, store storage.Storage, jsonlPath, gitRef string) error {
 	jsonlData, err := readFromGitRef(jsonlPath, gitRef)

cmd/bd/init.go

@@ -31,6 +31,10 @@ and database file. Optionally specify a custom issue prefix.
 
 With --no-db: creates .beads/ directory and issues.jsonl file instead of SQLite database.
 
+With --from-jsonl: imports from the current .beads/issues.jsonl file on disk instead
+of scanning git history. Use this after manual JSONL cleanup (e.g., bd compact --purge-tombstones)
+to prevent deleted issues from being resurrected during re-initialization.
+
 With --stealth: configures per-repository git settings for invisible beads usage:
   • .git/info/exclude to prevent beads files from being committed
   • Claude Code settings with bd onboard instruction
@@ -45,6 +49,7 @@ With --stealth: configures per-repository git settings for invisible beads usage
 		skipMergeDriver, _ := cmd.Flags().GetBool("skip-merge-driver")
 		skipHooks, _ := cmd.Flags().GetBool("skip-hooks")
 		force, _ := cmd.Flags().GetBool("force")
+		fromJSONL, _ := cmd.Flags().GetBool("from-jsonl")
 
 		// Initialize config (PersistentPreRun doesn't run for init command)
 		if err := config.Initialize(); err != nil {
@@ -385,20 +390,40 @@ With --stealth: configures per-repository git settings for invisible beads usage
 		}
 
 		// Check if git has existing issues to import (fresh clone scenario)
-		issueCount, jsonlPath, gitRef := checkGitForIssues()
+		// With --from-jsonl: import from local file instead of git history
-		if issueCount > 0 {
+		if fromJSONL {
-			if !quiet {
+			// Import from current working tree's JSONL file
-				fmt.Fprintf(os.Stderr, "\n✓ Database initialized. Found %d issues in git, importing...\n", issueCount)
+			localJSONLPath := filepath.Join(beadsDir, "issues.jsonl")
-			}
+			if _, err := os.Stat(localJSONLPath); err == nil {
-
+				issueCount, err := importFromLocalJSONL(ctx, initDBPath, store, localJSONLPath)
-			if err := importFromGit(ctx, initDBPath, store, jsonlPath, gitRef); err != nil {
+				if err != nil {
-				if !quiet {
+					if !quiet {
-					fmt.Fprintf(os.Stderr, "Warning: auto-import failed: %v\n", err)
+						fmt.Fprintf(os.Stderr, "Warning: import from local JSONL failed: %v\n", err)
-					fmt.Fprintf(os.Stderr, "Try manually: git show %s:%s | bd import -i /dev/stdin\n", gitRef, jsonlPath)
+					}
+					// Non-fatal - continue with empty database
+				} else if !quiet && issueCount > 0 {
+					fmt.Fprintf(os.Stderr, "✓ Imported %d issues from local %s\n\n", issueCount, localJSONLPath)
 				}
-				// Non-fatal - continue with empty database
 			} else if !quiet {
-				fmt.Fprintf(os.Stderr, "✓ Successfully imported %d issues from git.\n\n", issueCount)
+				fmt.Fprintf(os.Stderr, "Warning: --from-jsonl specified but %s not found\n", localJSONLPath)
+			}
+		} else {
+			// Default: import from git history
+			issueCount, jsonlPath, gitRef := checkGitForIssues()
+			if issueCount > 0 {
+				if !quiet {
+					fmt.Fprintf(os.Stderr, "\n✓ Database initialized. Found %d issues in git, importing...\n", issueCount)
+				}
+
+				if err := importFromGit(ctx, initDBPath, store, jsonlPath, gitRef); err != nil {
+					if !quiet {
+						fmt.Fprintf(os.Stderr, "Warning: auto-import failed: %v\n", err)
+						fmt.Fprintf(os.Stderr, "Try manually: git show %s:%s | bd import -i /dev/stdin\n", gitRef, jsonlPath)
+					}
+					// Non-fatal - continue with empty database
+				} else if !quiet {
+					fmt.Fprintf(os.Stderr, "✓ Successfully imported %d issues from git.\n\n", issueCount)
+				}
 			}
 		}
 
@@ -511,6 +536,7 @@ func init() {
 	initCmd.Flags().Bool("skip-hooks", false, "Skip git hooks installation")
 	initCmd.Flags().Bool("skip-merge-driver", false, "Skip git merge driver setup")
 	initCmd.Flags().Bool("force", false, "Force re-initialization even if JSONL already has issues (may cause data loss)")
+	initCmd.Flags().Bool("from-jsonl", false, "Import from current .beads/issues.jsonl file instead of git history (preserves manual cleanups)")
 	rootCmd.AddCommand(initCmd)
 }