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/config/config_test.go

@@ -37,7 +37,7 @@ func TestDefaults(t *testing.T) {
 		{"no-auto-import", false, func(k string) interface{} { return GetBool(k) }},
 		{"db", "", func(k string) interface{} { return GetString(k) }},
 		{"actor", "", func(k string) interface{} { return GetString(k) }},
-		{"flush-debounce", 5 * time.Second, func(k string) interface{} { return GetDuration(k) }},
+		{"flush-debounce", 30 * time.Second, func(k string) interface{} { return GetDuration(k) }},
 		{"auto-start-daemon", true, func(k string) interface{} { return GetBool(k) }},
 	}
 	

internal/rpc/rpc_test.go

@@ -435,10 +435,7 @@ func TestDatabaseHandshake(t *testing.T) {
 	os.MkdirAll(beadsDir1, 0750)
 	dbPath1 := filepath.Join(beadsDir1, "db1.db")
 	socketPath1 := filepath.Join(beadsDir1, "bd.sock")
-	store1, err := sqlitestorage.New(dbPath1)
-	if err != nil {
-		t.Fatalf("Failed to create store 1: %v", err)
-	}
+	store1 := newTestStore(t, dbPath1)
 	defer store1.Close()
 
 	server1 := NewServer(socketPath1, store1, tmpDir1, dbPath1)
@@ -453,10 +450,7 @@ func TestDatabaseHandshake(t *testing.T) {
 	os.MkdirAll(beadsDir2, 0750)
 	dbPath2 := filepath.Join(beadsDir2, "db2.db")
 	socketPath2 := filepath.Join(beadsDir2, "bd.sock")
-	store2, err := sqlitestorage.New(dbPath2)
-	if err != nil {
-		t.Fatalf("Failed to create store 2: %v", err)
-	}
+	store2 := newTestStore(t, dbPath2)
 	defer store2.Close()
 
 	server2 := NewServer(socketPath2, store2, tmpDir2, dbPath2)

internal/rpc/test_helpers.go

@@ -0,0 +1,28 @@
+package rpc
+
+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
+}

internal/rpc/version_test.go

@@ -85,10 +85,7 @@ func TestVersionCompatibility(t *testing.T) {
 			tmpDir, _, dbPath, socketPath, cleanup := setupTestServerIsolated(t)
 			defer cleanup()
 
-			store, err := sqlitestorage.New(dbPath)
-			if err != nil {
-				t.Fatalf("Failed to create store: %v", err)
-			}
+			store := newTestStore(t, dbPath)
 			defer store.Close()
 
 			// Override server version

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()