chore: Fix linting and formatting in server tests

- Remove unused imports (F401 errors)
- Remove unused variables (F841 errors)
- Apply black formatting to server code and tests
- Required for server-fast-automation.sh to pass

Author: Josh Bendson

src/code_indexer/server/app.py

@@ -1931,18 +1931,7 @@ def create_app() -> FastAPI:
     Returns:
         Configured FastAPI app
     """
-    global \
-        jwt_manager, \
-        user_manager, \
-        refresh_token_manager, \
-        golden_repo_manager, \
-        background_job_manager, \
-        activated_repo_manager, \
-        repository_listing_manager, \
-        semantic_query_manager, \
-        _server_start_time, \
-        _server_hnsw_cache, \
-        _server_fts_cache
+    global jwt_manager, user_manager, refresh_token_manager, golden_repo_manager, background_job_manager, activated_repo_manager, repository_listing_manager, semantic_query_manager, _server_start_time, _server_hnsw_cache, _server_fts_cache
 
     # Story #526: Initialize server-side HNSW cache at bootstrap for 1800x performance
     # Import and initialize global cache instance
@@ -5939,30 +5928,28 @@ async def semantic_query(
                 # Execute semantic search for hybrid or degraded mode
                 if search_mode_actual in ["semantic", "hybrid"]:
                     try:
-                        semantic_results_raw = (
-                            semantic_query_manager.query_user_repositories(
-                                username=current_user.username,
-                                query_text=request.query_text,
-                                repository_alias=request.repository_alias,
-                                limit=request.limit,
-                                min_score=request.min_score,
-                                file_extensions=request.file_extensions,
-                                # Phase 1 parameters (Story #503)
-                                exclude_language=request.exclude_language,
-                                exclude_path=request.exclude_path,
-                                accuracy=request.accuracy,
-                                # Temporal parameters (Story #446)
-                                time_range=request.time_range,
-                                time_range_all=request.time_range_all,
-                                at_commit=request.at_commit,
-                                include_removed=request.include_removed,
-                                show_evolution=request.show_evolution,
-                                evolution_limit=request.evolution_limit,
-                                # Phase 3 temporal filtering parameters (Story #503)
-                                diff_type=request.diff_type,
-                                author=request.author,
-                                chunk_type=request.chunk_type,
-                            )
+                        semantic_results_raw = semantic_query_manager.query_user_repositories(
+                            username=current_user.username,
+                            query_text=request.query_text,
+                            repository_alias=request.repository_alias,
+                            limit=request.limit,
+                            min_score=request.min_score,
+                            file_extensions=request.file_extensions,
+                            # Phase 1 parameters (Story #503)
+                            exclude_language=request.exclude_language,
+                            exclude_path=request.exclude_path,
+                            accuracy=request.accuracy,
+                            # Temporal parameters (Story #446)
+                            time_range=request.time_range,
+                            time_range_all=request.time_range_all,
+                            at_commit=request.at_commit,
+                            include_removed=request.include_removed,
+                            show_evolution=request.show_evolution,
+                            evolution_limit=request.evolution_limit,
+                            # Phase 3 temporal filtering parameters (Story #503)
+                            diff_type=request.diff_type,
+                            author=request.author,
+                            chunk_type=request.chunk_type,
                         )
                         semantic_results_list = [
                             QueryResultItem(**result)

src/code_indexer/server/auth/dependencies.py

@@ -549,7 +549,9 @@ async def _hybrid_auth_impl(
             else:
                 # Create User object from session
                 if not user_manager:
-                    logger.error(f"Hybrid auth ({auth_type}): user_manager not initialized")
+                    logger.error(
+                        f"Hybrid auth ({auth_type}): user_manager not initialized"
+                    )
                     raise HTTPException(
                         status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
                         detail="User manager not initialized",

src/code_indexer/server/jobs/manager.py

@@ -110,6 +110,7 @@ def __init__(
             from code_indexer.server.storage.sqlite_backends import (
                 SyncJobsSqliteBackend,
             )
+
             self._sqlite_backend = SyncJobsSqliteBackend(db_path)
 
         self._jobs: Dict[str, SyncJob] = {}
@@ -446,8 +447,14 @@ def create_job(
                     job_id=job_id,
                     username=username,
                     user_alias=user_alias,
-                    job_type=job_type.value if hasattr(job_type, "value") else str(job_type),
-                    status=initial_status.value if hasattr(initial_status, "value") else str(initial_status),
+                    job_type=(
+                        job_type.value if hasattr(job_type, "value") else str(job_type)
+                    ),
+                    status=(
+                        initial_status.value
+                        if hasattr(initial_status, "value")
+                        else str(initial_status)
+                    ),
                     repository_url=repository_url,
                 )
 
@@ -557,7 +564,11 @@ def mark_job_completed(
             if self._use_sqlite and self._sqlite_backend is not None:
                 self._sqlite_backend.update_job(
                     job_id=job_id,
-                    status=job.status.value if hasattr(job.status, "value") else str(job.status),
+                    status=(
+                        job.status.value
+                        if hasattr(job.status, "value")
+                        else str(job.status)
+                    ),
                     completed_at=completed_at.isoformat(),
                     progress=job.progress,
                     error_message=error_message,
@@ -619,7 +630,9 @@ def cancel_job(self, job_id: str) -> None:
                 self._sqlite_backend.update_job(
                     job_id=job_id,
                     status=JobStatus.CANCELLED.value,
-                    completed_at=job.completed_at.isoformat() if job.completed_at else None,
+                    completed_at=(
+                        job.completed_at.isoformat() if job.completed_at else None
+                    ),
                 )
 
             # Persist changes (JSON file, no-op for SQLite)

src/code_indexer/server/models/auto_discovery.py

@@ -18,33 +18,19 @@ class DiscoveredRepository(BaseModel):
     platform: Literal["gitlab", "github"] = Field(
         ..., description="Platform source (gitlab or github)"
     )
-    name: str = Field(
-        ..., min_length=1, description="Full path (e.g., group/project)"
-    )
-    description: Optional[str] = Field(
-        None, description="Project description"
-    )
-    clone_url_https: str = Field(
-        ..., description="HTTPS clone URL"
-    )
-    clone_url_ssh: str = Field(
-        ..., description="SSH clone URL"
-    )
-    default_branch: str = Field(
-        ..., description="Default branch (main/master/etc)"
-    )
+    name: str = Field(..., min_length=1, description="Full path (e.g., group/project)")
+    description: Optional[str] = Field(None, description="Project description")
+    clone_url_https: str = Field(..., description="HTTPS clone URL")
+    clone_url_ssh: str = Field(..., description="SSH clone URL")
+    default_branch: str = Field(..., description="Default branch (main/master/etc)")
     last_commit_hash: Optional[str] = Field(
         None, description="Short hash of last commit"
     )
-    last_commit_author: Optional[str] = Field(
-        None, description="Author of last commit"
-    )
+    last_commit_author: Optional[str] = Field(None, description="Author of last commit")
     last_activity: Optional[datetime] = Field(
         None, description="Last activity timestamp"
     )
-    is_private: bool = Field(
-        ..., description="Whether repository is private"
-    )
+    is_private: bool = Field(..., description="Whether repository is private")
 
     @field_validator("clone_url_https")
     @classmethod
@@ -72,18 +58,10 @@ class RepositoryDiscoveryResult(BaseModel):
     total_count: int = Field(
         ..., ge=0, description="Total number of repositories available"
     )
-    page: int = Field(
-        ..., ge=1, description="Current page number (1-indexed)"
-    )
-    page_size: int = Field(
-        ..., ge=1, description="Number of items per page"
-    )
-    total_pages: int = Field(
-        ..., ge=0, description="Total number of pages"
-    )
-    platform: Literal["gitlab", "github"] = Field(
-        ..., description="Platform source"
-    )
+    page: int = Field(..., ge=1, description="Current page number (1-indexed)")
+    page_size: int = Field(..., ge=1, description="Number of items per page")
+    total_pages: int = Field(..., ge=0, description="Total number of pages")
+    platform: Literal["gitlab", "github"] = Field(..., description="Platform source")
 
 
 class DiscoveryProviderError(BaseModel):
@@ -95,9 +73,5 @@ class DiscoveryProviderError(BaseModel):
     error_type: Literal["not_configured", "api_error", "auth_error", "timeout"] = Field(
         ..., description="Type of error"
     )
-    message: str = Field(
-        ..., description="Human-readable error message"
-    )
-    details: Optional[str] = Field(
-        None, description="Additional error details"
-    )
+    message: str = Field(..., description="Human-readable error message")
+    details: Optional[str] = Field(None, description="Additional error details")

src/code_indexer/server/multi/__init__.py

@@ -13,7 +13,12 @@
 from .multi_result_aggregator import MultiResultAggregator
 from .multi_search_service import MultiSearchService
 from .models import MultiSearchRequest, MultiSearchResponse, MultiSearchMetadata
-from .scip_models import SCIPMultiRequest, SCIPMultiResponse, SCIPMultiMetadata, SCIPResult
+from .scip_models import (
+    SCIPMultiRequest,
+    SCIPMultiResponse,
+    SCIPMultiMetadata,
+    SCIPResult,
+)
 from .scip_multi_service import SCIPMultiService
 
 __all__ = [

src/code_indexer/server/multi/models.py

@@ -58,7 +58,9 @@ class MultiSearchMetadata(BaseModel):
     """
 
     total_results: int = Field(..., description="Total number of results")
-    total_repos_searched: int = Field(..., description="Repositories successfully searched")
+    total_repos_searched: int = Field(
+        ..., description="Repositories successfully searched"
+    )
     execution_time_ms: int = Field(..., description="Execution time in milliseconds")
 
 

src/code_indexer/server/multi/multi_result_aggregator.py

@@ -31,7 +31,9 @@ def __init__(self, limit: int, min_score: Optional[float] = None):
         self.limit = limit
         self.min_score = min_score
 
-    def aggregate(self, repo_results: Dict[str, List[Dict[str, Any]]]) -> Dict[str, List[Dict[str, Any]]]:
+    def aggregate(
+        self, repo_results: Dict[str, List[Dict[str, Any]]]
+    ) -> Dict[str, List[Dict[str, Any]]]:
         """
         Aggregate results in per-repository mode with optional score filtering.
 

src/code_indexer/server/repositories/background_jobs.py

@@ -718,8 +718,12 @@ def _persist_jobs_sqlite(self) -> None:
                     self._sqlite_backend.update_job(
                         job_id=job_id,
                         status=job.status.value,
-                        started_at=job.started_at.isoformat() if job.started_at else None,
-                        completed_at=job.completed_at.isoformat() if job.completed_at else None,
+                        started_at=(
+                            job.started_at.isoformat() if job.started_at else None
+                        ),
+                        completed_at=(
+                            job.completed_at.isoformat() if job.completed_at else None
+                        ),
                         result=job.result,
                         error=job.error,
                         progress=job.progress,
@@ -737,8 +741,12 @@ def _persist_jobs_sqlite(self) -> None:
                         operation_type=job.operation_type,
                         status=job.status.value,
                         created_at=job.created_at.isoformat(),
-                        started_at=job.started_at.isoformat() if job.started_at else None,
-                        completed_at=job.completed_at.isoformat() if job.completed_at else None,
+                        started_at=(
+                            job.started_at.isoformat() if job.started_at else None
+                        ),
+                        completed_at=(
+                            job.completed_at.isoformat() if job.completed_at else None
+                        ),
                         result=job.result,
                         error=job.error,
                         progress=job.progress,

src/code_indexer/server/repositories/golden_repo_manager.py

@@ -1741,9 +1741,9 @@ async def get_golden_repo_branches(
             raise GoldenRepoError(f"Golden repository '{alias}' not found")
 
         branch_service = GoldenRepoBranchService(self)
-        branches: List[
-            "GoldenRepoBranchInfo"
-        ] = await branch_service.get_golden_repo_branches(alias)
+        branches: List["GoldenRepoBranchInfo"] = (
+            await branch_service.get_golden_repo_branches(alias)
+        )
         return branches
 
     def add_index_to_golden_repo(

src/code_indexer/server/services/claude_cli_manager.py

@@ -52,7 +52,9 @@ def __init__(self, api_key: Optional[str] = None, max_workers: int = 4):
         """
         self._api_key = api_key
         self._max_workers = max_workers
-        self._work_queue: "queue.Queue[Optional[Tuple[Path, Callable[[bool, str], None]]]]" = queue.Queue()
+        self._work_queue: (
+            "queue.Queue[Optional[Tuple[Path, Callable[[bool, str], None]]]]"
+        ) = queue.Queue()
         self._worker_threads: List[threading.Thread] = []
         self._shutdown_event = threading.Event()
         self._cli_available: Optional[bool] = None