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/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