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>

cmd/bd/comments_test.go

@@ -7,7 +7,6 @@ import (
 	"path/filepath"
 	"testing"
 
-	"github.com/steveyegge/beads/internal/storage/sqlite"
 	"github.com/steveyegge/beads/internal/types"
 )
 
@@ -21,10 +20,7 @@ func TestCommentsCommand(t *testing.T) {
 	defer os.RemoveAll(tmpDir)
 
 	testDB := filepath.Join(tmpDir, "test.db")
-	s, err := sqlite.New(testDB)
-	if err != nil {
-		t.Fatalf("Failed to create store: %v", err)
-	}
+	s := newTestStore(t, testDB)
 	defer s.Close()
 
 	ctx := context.Background()

cmd/bd/direct_mode_test.go

@@ -8,7 +8,6 @@ import (
 	"testing"
 
 	"github.com/steveyegge/beads/internal/rpc"
-	"github.com/steveyegge/beads/internal/storage/sqlite"
 	"github.com/steveyegge/beads/internal/types"
 )
 
@@ -67,10 +66,7 @@ func TestFallbackToDirectModeEnablesFlush(t *testing.T) {
 	testDBPath := filepath.Join(beadsDir, "test.db")
 
 	// Seed database with issues
-	setupStore, err := sqlite.New(testDBPath)
-	if err != nil {
-		t.Fatalf("failed to create seed store: %v", err)
-	}
+	setupStore := newTestStore(t, testDBPath)
 
 	ctx := context.Background()
 	target := &types.Issue{

cmd/bd/export_test.go

@@ -8,7 +8,6 @@ import (
 	"path/filepath"
 	"testing"
 
-	"github.com/steveyegge/beads/internal/storage/sqlite"
 	"github.com/steveyegge/beads/internal/types"
 )
 
@@ -22,10 +21,7 @@ func TestExportCommand(t *testing.T) {
 	defer os.RemoveAll(tmpDir)
 
 	testDB := filepath.Join(tmpDir, "test.db")
-	s, err := sqlite.New(testDB)
-	if err != nil {
-		t.Fatalf("Failed to create store: %v", err)
-	}
+	s := newTestStore(t, testDB)
 	defer s.Close()
 
 	ctx := context.Background()
@@ -228,10 +224,7 @@ func TestExportCommand(t *testing.T) {
 
 		// Create empty database
 		emptyDBPath := filepath.Join(tmpDir, "empty.db")
-		emptyStore, err := sqlite.New(emptyDBPath)
-		if err != nil {
-			t.Fatalf("Failed to create empty store: %v", err)
-		}
+		emptyStore := newTestStore(t, emptyDBPath)
 		defer emptyStore.Close()
 
 		// Test using exportToJSONLWithStore directly (daemon code path)

cmd/bd/git_sync_test.go

@@ -45,10 +45,7 @@ func TestGitPullSyncIntegration(t *testing.T) {
 	}
 	
 	clone1DBPath := filepath.Join(clone1BeadsDir, "test.db")
-	clone1Store, err := sqlite.New(clone1DBPath)
-	if err != nil {
-		t.Fatalf("Failed to create clone1 database: %v", err)
-	}
+	clone1Store := newTestStore(t, clone1DBPath)
 	defer clone1Store.Close()
 	
 	ctx := context.Background()
@@ -94,10 +91,7 @@ func TestGitPullSyncIntegration(t *testing.T) {
 	// Initialize empty database in clone2
 	clone2BeadsDir := filepath.Join(clone2Dir, ".beads")
 	clone2DBPath := filepath.Join(clone2BeadsDir, "test.db")
-	clone2Store, err := sqlite.New(clone2DBPath)
-	if err != nil {
-		t.Fatalf("Failed to create clone2 database: %v", err)
-	}
+	clone2Store := newTestStore(t, clone2DBPath)
 	defer clone2Store.Close()
 	
 	if err := clone2Store.SetMetadata(ctx, "issue_prefix", "test"); err != nil {
@@ -141,10 +135,7 @@ func TestGitPullSyncIntegration(t *testing.T) {
 		
 		// In real usage, auto-import would trigger on next bd command
 		// For this test, we'll manually import to simulate that behavior
-		newStore, err := sqlite.New(clone2DBPath)
-		if err != nil {
-			t.Fatalf("Failed to reopen database: %v", err)
-		}
+		newStore := newTestStore(t, clone2DBPath)
 		// Don't defer close - we'll reassign to clone2Store for the next test
 		
 		// Manually import to simulate auto-import behavior

cmd/bd/label_test.go

@@ -123,10 +123,7 @@ func TestLabelCommands(t *testing.T) {
 	defer os.RemoveAll(tmpDir)
 
 	testDB := filepath.Join(tmpDir, "test.db")
-	s, err := sqlite.New(testDB)
-	if err != nil {
-		t.Fatalf("Failed to create store: %v", err)
-	}
+	s := newTestStore(t, testDB)
 	defer s.Close()
 
 	ctx := context.Background()

cmd/bd/list_test.go

@@ -98,10 +98,7 @@ func TestListCommand(t *testing.T) {
 	defer os.RemoveAll(tmpDir)
 
 	testDB := filepath.Join(tmpDir, "test.db")
-	s, err := sqlite.New(testDB)
-	if err != nil {
-		t.Fatalf("Failed to create store: %v", err)
-	}
+	s := newTestStore(t, testDB)
 	defer s.Close()
 
 	h := newListTestHelper(t, s)

cmd/bd/reopen_test.go

@@ -101,10 +101,7 @@ func TestReopenCommand(t *testing.T) {
 	defer os.RemoveAll(tmpDir)
 
 	testDB := filepath.Join(tmpDir, "test.db")
-	s, err := sqlite.New(testDB)
-	if err != nil {
-		t.Fatalf("Failed to create store: %v", err)
-	}
+	s := newTestStore(t, testDB)
 	defer s.Close()
 
 	ctx := context.Background()