Fix bd-166: Prevent duplicate issues with wrong prefix

Critical fix for silent data corruption where database created 173
duplicate issues with wrong prefix (beads- instead of bd-).

Root cause: When issue_prefix config was missing, CreateIssue fell
back to deriving prefix from database filename (beads.db → 'beads'),
while auto-import imported bd- issues from git with SkipPrefixValidation.
This created duplicates.

Changes:
1. Removed derivePrefixFromPath() - never derive prefix from filename
2. CreateIssue/CreateIssues now REJECT if issue_prefix config missing
   - Fail-fast with clear error message
3. Auto-import now SETS issue_prefix from first imported issue if missing
   - Handles fresh clone scenario safely
4. Added newTestStore() helper that sets issue_prefix for tests
5. Updated test setup in multiple files to prevent test failures

Follow-ups filed: bd-167, bd-168, bd-169

Closes bd-166

Amp-Thread-ID: https://ampcode.com/threads/T-b2ee0738-b90b-40ef-ae44-f2d93729842c
Co-authored-by: Amp <amp@ampcode.com>

cmd/bd/autoimport.go

@@ -9,6 +9,7 @@ import (
 	"os"
 	"os/exec"
 	"path/filepath"
+	"strings"
 
 	"github.com/steveyegge/beads/internal/storage"
 	"github.com/steveyegge/beads/internal/types"
@@ -167,7 +168,24 @@ func importFromGit(ctx context.Context, dbFilePath string, store storage.Storage
 		return fmt.Errorf("failed to scan JSONL: %w", err)
 	}
 
+	// CRITICAL (bd-166): Set issue_prefix from first imported issue if missing
+	// This prevents derivePrefixFromPath fallback which caused duplicate issues
+	if len(issues) > 0 {
+		configuredPrefix, err := store.GetConfig(ctx, "issue_prefix")
+		if err == nil && strings.TrimSpace(configuredPrefix) == "" {
+			// Database has no prefix configured - derive from first issue
+			firstPrefix := extractPrefix(issues[0].ID)
+			if firstPrefix != "" {
+				if err := store.SetConfig(ctx, "issue_prefix", firstPrefix); err != nil {
+					return fmt.Errorf("failed to set issue_prefix from imported issues: %w", err)
+				}
+			}
+		}
+	}
+
 	// Use existing import logic with auto-resolve collisions
+	// Note: SkipPrefixValidation allows mixed prefixes during auto-import
+	// (but now we set the prefix first, so CreateIssue won't use filename fallback)
 	opts := ImportOptions{
 		ResolveCollisions:  true,
 		DryRun:             false,

cmd/bd/config_test.go

@@ -162,6 +162,14 @@ func setupTestDB(t *testing.T) (*sqlite.SQLiteStorage, func()) {
 		t.Fatalf("Failed to create test database: %v", err)
 	}
 
+	// CRITICAL (bd-166): Set issue_prefix to prevent "database not initialized" errors
+	ctx := context.Background()
+	if err := store.SetConfig(ctx, "issue_prefix", "bd"); err != nil {
+		store.Close()
+		os.RemoveAll(tmpDir)
+		t.Fatalf("Failed to set issue_prefix: %v", err)
+	}
+
 	cleanup := func() {
 		store.Close()
 		os.RemoveAll(tmpDir)

cmd/bd/daemon_test.go

@@ -161,10 +161,7 @@ func TestDaemonIntegration(t *testing.T) {
 	}
 
 	testDBPath := filepath.Join(dbDir, "test.db")
-	testStore, err := sqlite.New(testDBPath)
-	if err != nil {
-		t.Fatalf("Failed to create test database: %v", err)
-	}
+	testStore := newTestStore(t, testDBPath)
 
 	oldStore := store
 	oldDBPath := dbPath
@@ -305,10 +302,7 @@ func TestDaemonRPCServerIntegration(t *testing.T) {
 	}
 
 	testDBPath := filepath.Join(dbDir, "test.db")
-	testStore, err := sqlite.New(testDBPath)
-	if err != nil {
-		t.Fatalf("Failed to create test database: %v", err)
-	}
+	testStore := newTestStore(t, testDBPath)
 	defer testStore.Close()
 
 	ctx, cancel := context.WithTimeout(context.Background(), 10*time.Second)
@@ -342,10 +336,7 @@ func TestDaemonConcurrentOperations(t *testing.T) {
 	}
 
 	testDBPath := filepath.Join(dbDir, "test.db")
-	testStore, err := sqlite.New(testDBPath)
-	if err != nil {
-		t.Fatalf("Failed to create test database: %v", err)
-	}
+	testStore := newTestStore(t, testDBPath)
 	defer testStore.Close()
 
 	ctx := context.Background()
@@ -410,10 +401,7 @@ func TestDaemonSocketCleanupOnShutdown(t *testing.T) {
 	socketPath := filepath.Join(tmpDir, "test.sock")
 	testDBPath := filepath.Join(tmpDir, "test.db")
 
-	testStore, err := sqlite.New(testDBPath)
-	if err != nil {
-		t.Fatalf("Failed to create test database: %v", err)
-	}
+	testStore := newTestStore(t, testDBPath)
 
 	server := newMockDaemonServer(socketPath, testStore)
 
@@ -543,10 +531,7 @@ func TestDaemonGracefulShutdown(t *testing.T) {
 	socketPath := filepath.Join(tmpDir, "test.sock")
 	testDBPath := filepath.Join(tmpDir, "test.db")
 
-	testStore, err := sqlite.New(testDBPath)
-	if err != nil {
-		t.Fatalf("Failed to create test database: %v", err)
-	}
+	testStore := newTestStore(t, testDBPath)
 
 	server := newMockDaemonServer(socketPath, testStore)
 

cmd/bd/test_helpers_test.go

@@ -0,0 +1,28 @@
+package main
+
+import (
+	"context"
+	"testing"
+
+	"github.com/steveyegge/beads/internal/storage/sqlite"
+)
+
+// newTestStore creates a SQLite store with issue_prefix configured (bd-166)
+// This prevents "database not initialized" errors in tests
+func newTestStore(t *testing.T, dbPath string) *sqlite.SQLiteStorage {
+	t.Helper()
+	
+	store, err := sqlite.New(dbPath)
+	if err != nil {
+		t.Fatalf("Failed to create test database: %v", err)
+	}
+	
+	// CRITICAL (bd-166): Set issue_prefix to prevent "database not initialized" errors
+	ctx := context.Background()
+	if err := store.SetConfig(ctx, "issue_prefix", "bd"); err != nil {
+		store.Close()
+		t.Fatalf("Failed to set issue_prefix: %v", err)
+	}
+	
+	return store
+}