fix: Comprehensive linting and formatting cleanup

- Fixed 678 linting errors automatically with ruff
- Applied black formatting to 50 files
- Fixed critical undefined names and missing imports
- Added missing type annotations and imports
- Fixed indentation issues in context_managers.py
- Added sklearn import for cosine_similarity
- Resolved TypeVar and ParamSpec imports in decorators
- Added missing Observable and Priority classes

Remaining issues are mostly style improvements (type hints, deprecations)
that don't affect functionality

Author: raold

.claude/settings.local.json

@@ -119,7 +119,15 @@
       "Bash(cmd.exe /c start http://localhost:8001/docs)",
       "Bash(pg_isready:*)",
       "Bash(./start_postgres_only.sh:*)",
-      "Bash(git config:*)"
+      "Bash(git config:*)",
+      "Bash(cd:*)",
+      "Bash(cd:*)",
+      "Bash(cd:*)",
+      "Bash(cd:*)",
+      "Bash(cd:*)",
+      "Bash(cd:*)",
+      "Bash(cd:*)",
+      "Bash(cd:*)"
     ],
     "deny": []
   }

app/__init__.py

@@ -6,4 +6,4 @@
 __version__ = "4.0.0"
 __author__ = "raold"
 __email__ = "dro@lynchburgsmiles.com"
-__description__ = "AI-powered second brain with Cipher memory integration"
+__description__ = "AI-powered second brain with Cipher memory integration"

app/app.py

@@ -5,14 +5,10 @@
 No circular imports, no bullshit, just clean code that works.
 """
 
-import os
 from contextlib import asynccontextmanager
-from datetime import datetime
-from pathlib import Path
 
-from fastapi import FastAPI, HTTPException, Depends
+from fastapi import FastAPI
 from fastapi.middleware.cors import CORSMiddleware
-from pydantic import BaseModel
 
 # Version info
 __version__ = "4.0.0"
@@ -27,9 +23,9 @@ async def lifespan(app: FastAPI):
     """Handle application startup and shutdown."""
     # Startup
     print(f"🚀 Starting Second Brain v{__version__}")
-    
+
     yield
-    
+
     # Shutdown
     print("👋 Shutting down Second Brain")
 
@@ -65,12 +61,13 @@ def include_routers():
     try:
         # Setup dependencies first
         setup_dependencies()
-        
+
         # V2 API routes - the ONLY implementation we use
         from app.routes.v2_api import router
+
         app.include_router(router, prefix="")
         print("✅ V2 API routes included")
-        
+
     except Exception as e:
         print(f"⚠️ Error including routers: {e}")
         # Continue anyway - app will work with basic endpoints
@@ -88,22 +85,19 @@ async def root():
         "message": "Welcome to Second Brain API v2",
         "version": __version__,
         "docs": "/docs",
-        "health": "/api/v2/health"
+        "health": "/api/v2/health",
     }
 
 
 # Error handling
 @app.exception_handler(Exception)
 async def general_exception_handler(request, exc):
     """Handle all uncaught exceptions."""
-    return {
-        "error": "Internal server error",
-        "message": str(exc),
-        "type": type(exc).__name__
-    }
+    return {"error": "Internal server error", "message": str(exc), "type": type(exc).__name__}
 
 
 if __name__ == "__main__":
     # For testing only
     import uvicorn
-    uvicorn.run(app, host="0.0.0.0", port=8000)
+
+    uvicorn.run(app, host="0.0.0.0", port=8000)

app/config.py

@@ -3,7 +3,7 @@
 Uses the centralized environment manager for consistent configuration.
 """
 
-from app.core.env_manager import get_env_manager, Environment
+from app.core.env_manager import Environment, get_env_manager
 
 # Get environment manager instance
 env = get_env_manager()
@@ -14,49 +14,51 @@ class Config:
     Application configuration using environment manager.
     All environment variables are accessed through the centralized manager.
     """
-    
+
     # Environment
     ENVIRONMENT: Environment = env.environment
     IS_PRODUCTION: bool = env.is_production()
     IS_DEVELOPMENT: bool = env.is_development()
     IS_TEST: bool = env.is_test()
-    
+
     # Database Configuration
     DATABASE_URL: str = env.get_database_url()
-    
+
     # PostgreSQL Configuration (individual components)
     POSTGRES_USER: str = env.get("POSTGRES_USER", "postgres")
     POSTGRES_PASSWORD: str = env.get("POSTGRES_PASSWORD", "postgres")
     POSTGRES_HOST: str = env.get("POSTGRES_HOST", "localhost")
     POSTGRES_PORT: str = env.get("POSTGRES_PORT", "5432")
     POSTGRES_DB: str = env.get("POSTGRES_DB", "secondbrain")
-    
+
     # Redis removed - using PostgreSQL for everything
-    
+
     # OpenAI Configuration
     OPENAI_API_KEY: str = env.get("OPENAI_API_KEY", "")
     OPENAI_EMBEDDING_MODEL: str = env.get("OPENAI_EMBEDDING_MODEL", "text-embedding-3-small")
     OPENAI_CHAT_MODEL: str = env.get("OPENAI_CHAT_MODEL", "gpt-4")
-    
+
     # Anthropic Configuration (Optional)
     ANTHROPIC_API_KEY: str = env.get("ANTHROPIC_API_KEY", "")
-    
+
     # Container Security (Single User)
     CONTAINER_API_KEY: str = env.get("CONTAINER_API_KEY", "")
     # JWT removed - not needed for single user containers
-    
+
     # API Configuration
     API_TOKENS: list = env.get_list("API_TOKENS", [])
-    
+
     # Application Configuration
     HOST: str = env.get("HOST", "127.0.0.1")
     PORT: int = env.get_int("PORT", 8000)
     DEBUG: bool = env.get_bool("DEBUG", False)
     LOG_LEVEL: str = env.get("LOG_LEVEL", "INFO")
-    
+
     # CORS Configuration
-    CORS_ORIGINS: list = env.get_list("CORS_ORIGINS", ["http://localhost:3000", "http://localhost:8000"])
-    
+    CORS_ORIGINS: list = env.get_list(
+        "CORS_ORIGINS", ["http://localhost:3000", "http://localhost:8000"]
+    )
+
     # Feature Flags
     # NO MOCKS - PostgreSQL ONLY
     USE_MOCK_DATABASE: bool = False
@@ -65,46 +67,46 @@ class Config:
     FEATURE_ATTACHMENTS_ENABLED: bool = env.get_bool("FEATURE_ATTACHMENTS_ENABLED", True)
     ENABLE_TELEMETRY: bool = env.get_bool("ENABLE_TELEMETRY", False)
     ENABLE_ANALYTICS: bool = env.get_bool("ENABLE_ANALYTICS", False)
-    
+
     # AI Model Configuration
     VECTOR_DIMENSION: int = env.get_int("VECTOR_DIMENSION", 1536)
     BATCH_SIZE: int = env.get_int("BATCH_SIZE", 100)
     SIMILARITY_THRESHOLD: float = env.get_float("SIMILARITY_THRESHOLD", 0.7)
-    
+
     # Monitoring Configuration
     OTEL_EXPORTER_OTLP_ENDPOINT: str = env.get("OTEL_EXPORTER_OTLP_ENDPOINT", "")
     OTEL_SERVICE_NAME: str = env.get("OTEL_SERVICE_NAME", "second-brain")
     SENTRY_DSN: str = env.get("SENTRY_DSN", "")
-    
+
     # Development Configuration
     ENABLE_HOT_RELOAD: bool = env.get_bool("ENABLE_HOT_RELOAD", IS_DEVELOPMENT)
     ENABLE_DEBUG_TOOLBAR: bool = env.get_bool("ENABLE_DEBUG_TOOLBAR", False)
-    
+
     @classmethod
     def validate(cls) -> list:
         """
         Validate configuration for production readiness.
-        
+
         Returns:
             List of validation issues (empty if valid)
         """
         return env.validate_production_ready()
-    
+
     @classmethod
     def get_summary(cls) -> dict:
         """
         Get configuration summary for logging.
-        
+
         Returns:
             Dictionary of configuration values (sensitive values masked)
         """
         return env.get_config_summary()
-    
+
     @classmethod
     def is_ai_enabled(cls) -> bool:
         """Check if AI features are enabled."""
         return bool(cls.OPENAI_API_KEY) or cls.USE_MOCK_OPENAI
-    
+
     @classmethod
     def is_database_configured(cls) -> bool:
         """Check if database is configured."""
@@ -114,4 +116,4 @@ def is_database_configured(cls) -> bool:
 # Convenience function for backward compatibility
 def get_config() -> Config:
     """Get configuration instance."""
-    return Config
+    return Config

app/core/__init__.py

@@ -2,4 +2,4 @@
 Core application infrastructure
 """
 
-# Core module - simplified for single-user architecture
+# Core module - simplified for single-user architecture