fix(init): allow fresh clones with JSONL to run bd init (bd-4h9)

Previously, bd init blocked when JSONL existed with issues but no database,
telling users to run 'bd doctor --fix'. But doctor --fix just ran bd migrate
which requires an existing database - creating a circular dependency.

Now:
- bd init allows fresh clones (JSONL exists, no database) to proceed
- bd init creates the database and imports from JSONL automatically
- bd doctor --fix runs bd init (not migrate) when there's no database

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

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

.beads/deletions.jsonl

@@ -94,3 +94,4 @@
 {"id":"bd-tjn","ts":"2025-12-01T05:13:13.738456Z","by":"git-history-backfill","reason":"recovered from git history (pruned from manifest)"}
 {"id":"bd-qvj","ts":"2025-12-01T05:13:13.743949Z","by":"git-history-backfill","reason":"recovered from git history (pruned from manifest)"}
 {"id":"bd-clg","ts":"2025-12-01T05:13:13.748995Z","by":"git-history-backfill","reason":"recovered from git history (pruned from manifest)"}
+{"id":"bd-4h9","ts":"2025-12-01T05:18:00.744362Z","by":"git-history-backfill","reason":"recovered from git history (pruned from manifest)"}

cmd/bd/doctor/fix/migrate.go

@@ -4,9 +4,11 @@ import (
 	"fmt"
 	"os"
 	"os/exec"
+	"path/filepath"
 )
 
-// DatabaseVersion fixes database version mismatches by running bd migrate
+// DatabaseVersion fixes database version mismatches by running bd migrate,
+// or creates the database from JSONL by running bd init for fresh clones (bd-4h9).
 func DatabaseVersion(path string) error {
 	// Validate workspace
 	if err := validateBeadsWorkspace(path); err != nil {
@@ -19,7 +21,25 @@ func DatabaseVersion(path string) error {
 		return err
 	}
 
-	// Run bd migrate
+	// Check if database exists - if not, run init instead of migrate (bd-4h9)
+	beadsDir := filepath.Join(path, ".beads")
+	dbPath := filepath.Join(beadsDir, "beads.db")
+
+	if _, err := os.Stat(dbPath); os.IsNotExist(err) {
+		// No database - this is a fresh clone, run bd init
+		fmt.Println("→ No database found, running 'bd init' to hydrate from JSONL...")
+		cmd := exec.Command(bdBinary, "init") // #nosec G204 -- bdBinary from validated executable path
+		cmd.Dir = path
+		cmd.Stdout = os.Stdout
+		cmd.Stderr = os.Stderr
+
+		if err := cmd.Run(); err != nil {
+			return fmt.Errorf("failed to initialize database: %w", err)
+		}
+		return nil
+	}
+
+	// Database exists - run bd migrate
 	cmd := exec.Command(bdBinary, "migrate") // #nosec G204 -- bdBinary from validated executable path
 	cmd.Dir = path                           // Set working directory without changing process dir
 	cmd.Stdout = os.Stdout

cmd/bd/init.go

@@ -1338,8 +1338,12 @@ func setupGlobalGitIgnore(homeDir string, verbose bool) error {
 	return nil
 }
 
-// checkExistingBeadsData checks for existing JSONL or database files
+// checkExistingBeadsData checks for existing database files
 // and returns an error if found (safety guard for bd-emg)
+//
+// Note: This only blocks when a database already exists (workspace is initialized).
+// Fresh clones with JSONL but no database are allowed - init will create the database
+// and import from JSONL automatically (bd-4h9: fixes circular dependency with doctor --fix).
 func checkExistingBeadsData(prefix string) error {
 	cwd, err := os.Getwd()
 	if err != nil {
@@ -1373,44 +1377,12 @@ To completely reinitialize (data loss warning):
 Aborting.`, yellow("⚠"), dbPath, cyan("bd list"), prefix)
 	}
 
-	// Check for existing JSONL files with issues
+	// Fresh clones (JSONL exists but no database) are allowed - init will
-	jsonlCandidates := []string{
+	// create the database and import from JSONL automatically.
-		filepath.Join(beadsDir, "issues.jsonl"),
+	// This fixes the circular dependency where init told users to run
-		filepath.Join(beadsDir, "beads.jsonl"),
+	// "bd doctor --fix" but doctor couldn't create a database (bd-4h9).
-	}
 
-	for _, jsonlPath := range jsonlCandidates {
+	return nil // No database found, safe to init
-		if _, err := os.Stat(jsonlPath); err == nil {
-			// JSONL exists, count issues
-			issueCount := countIssuesInJSONLFile(jsonlPath)
-
-			if issueCount > 0 {
-				yellow := color.New(color.FgYellow).SprintFunc()
-				cyan := color.New(color.FgCyan).SprintFunc()
-
-				prefixHint := prefix
-				if prefixHint == "" {
-					prefixHint = "<prefix>"
-				}
-
-				return fmt.Errorf(`
-%s Found existing %s with %d issues.
-
-This appears to be a fresh clone, not a new project.
-
-To hydrate the database from existing JSONL:
-  %s
-
-To force re-initialization (may cause data loss):
-  bd init --prefix %s --force
-
-Aborting.`, yellow("⚠"), filepath.Base(jsonlPath), issueCount, cyan("bd doctor --fix"), prefixHint)
-			}
-			// Empty JSONL (0 issues) is OK - likely a new project
-		}
-	}
-
-	return nil // No existing data found, safe to init
 }