Fix all test failures from bd-166 (missing issue_prefix)

Completed bd-167: Fixed all tests that failed with 'database not initialized: issue_prefix config is missing' error.

Changes:
- Created test helper functions in 3 locations:
  * cmd/bd/test_helpers_test.go (already existed)
  * internal/rpc/test_helpers.go (new)
  * internal/storage/sqlite/test_helpers.go (new)

- Updated all affected test files to use newTestStore():
  * cmd/bd: comments, export, git_sync, label, list, reopen, direct_mode
  * internal/rpc: rpc_test, version_test
  * internal/storage/sqlite: sqlite_test, underlying_db_test

- Fixed config test: updated flush-debounce default from 5s to 30s

- Removed unused sqlite imports from test files

All tests now passing ✅

Also:
- Closed bd-167, bd-170 (cleanup of beads-* duplicates)
- Removed corrupt backup files

Amp-Thread-ID: https://ampcode.com/threads/T-4a8c6002-9384-45b6-81f6-2907d1e4c6c2
Co-authored-by: Amp <amp@ampcode.com>

internal/storage/sqlite/sqlite_test.go

@@ -1301,6 +1301,11 @@ func TestInMemoryDatabase(t *testing.T) {
 	}
 	defer store.Close()
 
+	// Set issue_prefix (bd-166)
+	if err := store.SetConfig(ctx, "issue_prefix", "bd"); err != nil {
+		t.Fatalf("failed to set issue_prefix: %v", err)
+	}
+
 	// Verify we can create and retrieve an issue
 	issue := &types.Issue{
 		Title:       "Test in-memory issue",
@@ -1344,6 +1349,11 @@ func TestInMemorySharedCache(t *testing.T) {
 	}
 	defer store1.Close()
 
+	// Set issue_prefix (bd-166)
+	if err := store1.SetConfig(ctx, "issue_prefix", "bd"); err != nil {
+		t.Fatalf("failed to set issue_prefix: %v", err)
+	}
+
 	// Create an issue in the first connection
 	issue := &types.Issue{
 		Title:       "Shared memory test",

internal/storage/sqlite/test_helpers.go

@@ -0,0 +1,26 @@
+package sqlite
+
+import (
+	"context"
+	"testing"
+)
+
+// newTestStore creates a SQLiteStorage with issue_prefix configured (bd-166)
+// This prevents "database not initialized" errors in tests
+func newTestStore(t *testing.T, dbPath string) *SQLiteStorage {
+	t.Helper()
+	
+	store, err := 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
+}

internal/storage/sqlite/underlying_db_test.go

@@ -20,10 +20,7 @@ func TestUnderlyingDB_BasicAccess(t *testing.T) {
 	defer os.RemoveAll(tmpDir)
 
 	dbPath := filepath.Join(tmpDir, "test.db")
-	store, err := New(dbPath)
-	if err != nil {
-		t.Fatalf("Failed to create storage: %v", err)
-	}
+	store := newTestStore(t, dbPath)
 	defer store.Close()
 
 	// Get underlying DB
@@ -53,10 +50,7 @@ func TestUnderlyingDB_CreateExtensionTable(t *testing.T) {
 	defer os.RemoveAll(tmpDir)
 
 	dbPath := filepath.Join(tmpDir, "test.db")
-	store, err := New(dbPath)
-	if err != nil {
-		t.Fatalf("Failed to create storage: %v", err)
-	}
+	store := newTestStore(t, dbPath)
 	defer store.Close()
 
 	ctx := context.Background()
@@ -145,10 +139,7 @@ func TestUnderlyingDB_ConcurrentAccess(t *testing.T) {
 	defer os.RemoveAll(tmpDir)
 
 	dbPath := filepath.Join(tmpDir, "test.db")
-	store, err := New(dbPath)
-	if err != nil {
-		t.Fatalf("Failed to create storage: %v", err)
-	}
+	store := newTestStore(t, dbPath)
 	defer store.Close()
 
 	ctx := context.Background()
@@ -243,10 +234,7 @@ func TestUnderlyingDB_LongTxDoesNotDeadlock(t *testing.T) {
 	defer os.RemoveAll(tmpDir)
 
 	dbPath := filepath.Join(tmpDir, "test.db")
-	store, err := New(dbPath)
-	if err != nil {
-		t.Fatalf("Failed to create storage: %v", err)
-	}
+	store := newTestStore(t, dbPath)
 	defer store.Close()
 
 	ctx := context.Background()
@@ -297,10 +285,7 @@ func TestUnderlyingConn_BasicAccess(t *testing.T) {
 	defer os.RemoveAll(tmpDir)
 
 	dbPath := filepath.Join(tmpDir, "test.db")
-	store, err := New(dbPath)
-	if err != nil {
-		t.Fatalf("Failed to create storage: %v", err)
-	}
+	store := newTestStore(t, dbPath)
 	defer store.Close()
 
 	ctx := context.Background()
@@ -333,10 +318,7 @@ func TestUnderlyingConn_DDLOperations(t *testing.T) {
 	defer os.RemoveAll(tmpDir)
 
 	dbPath := filepath.Join(tmpDir, "test.db")
-	store, err := New(dbPath)
-	if err != nil {
-		t.Fatalf("Failed to create storage: %v", err)
-	}
+	store := newTestStore(t, dbPath)
 	defer store.Close()
 
 	ctx := context.Background()
@@ -417,10 +399,7 @@ func TestUnderlyingConn_ContextCancellation(t *testing.T) {
 	defer os.RemoveAll(tmpDir)
 
 	dbPath := filepath.Join(tmpDir, "test.db")
-	store, err := New(dbPath)
-	if err != nil {
-		t.Fatalf("Failed to create storage: %v", err)
-	}
+	store := newTestStore(t, dbPath)
 	defer store.Close()
 
 	// Create a context that's already canceled
@@ -444,10 +423,7 @@ func TestUnderlyingConn_MultipleConnections(t *testing.T) {
 	defer os.RemoveAll(tmpDir)
 
 	dbPath := filepath.Join(tmpDir, "test.db")
-	store, err := New(dbPath)
-	if err != nil {
-		t.Fatalf("Failed to create storage: %v", err)
-	}
+	store := newTestStore(t, dbPath)
 	defer store.Close()
 
 	ctx := context.Background()