Config Refactor: unify config handling

- Consolidated all system/user config logic into configmanager.py
- Removed duplicate loaders from setup.py and TUI.py
- Eliminated .env redundancy; now only stores WORKING_DIR
- Clarified boundaries: system config immutable, user config mutable
- Updated TUI to use save_user_config()
- Removed all deprecated/legacy config functions and aliases

utils/setup.py

@@ -13,18 +13,20 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program. If not, see <https://www.gnu.org/licenses/>.
 
-import json
 import logging
 import logging.config
 import logging.handlers
 import os
 from pathlib import Path
 import platform
-import sys
 
 from dotenv import load_dotenv, set_key
 
-from utils.configmanager import PROTECTED_KEYS, load_protected_config
+from utils.configmanager import (
+    get_system_value,
+    load_system_config,
+    load_user_config,
+)
 
 
 def get_base_directory() -> Path:
@@ -38,7 +40,7 @@ def get_base_directory() -> Path:
         return home / ".local" / "share" / "Loxide"
 
 
-def configure_logging(log_dir: Path, log_level: str = "DEBUG"):
+def configure_logging(log_dir: Path, log_level: str = "INFO"):
     log_file = log_dir / "Loxide.log"
 
     config = {
@@ -62,12 +64,12 @@ def configure_logging(log_dir: Path, log_level: str = "DEBUG"):
                 "interval": 1,  # Every 1 day
                 "backupCount": 7,  # Keep 7 days of logs
                 "encoding": "utf-8",  # Ensure UTF-8 encoding
-                "level": "DEBUG",  # Always log DEBUG and above
+                "level": "DEBUG",  # Always log DEBUG and above to file
                 "formatter": "detailed",  # Use detailed format
             },
             "console": {
                 "class": "logging.StreamHandler",
-                "level": log_level.upper(),  # Configurable log level
+                "level": log_level.upper(),  # System-configured level for console
                 "formatter": "simple",  # Use simple format
             },
         },
@@ -95,59 +97,15 @@ def configure_logging(log_dir: Path, log_level: str = "DEBUG"):
     logging.getLogger().debug("✅ Logging configured.")
 
 
-def get_system_config_path() -> Path:
-    base_path = Path(
-        getattr(sys, "_MEIPASS", os.path.dirname(os.path.abspath(__file__)))
-    )
-    return base_path.parent / "system_config.json"
-
-
-def load_system_config() -> dict:
-    try:
-        config_path = get_system_config_path()
-        with open(config_path, "r") as f:
-            return json.load(f)
-    except FileNotFoundError:
-        logging.warning("⚠️ system_config.json not found. Using built-in defaults.")
-        return {
-            "APPNAME": "Loxide",
-            "LOG_LEVEL": "DEBUG",
-            "PATH_EXCLUSION_CONST": 4,
-            "MIN_FILES_FOR_PATH": 4,
-            "VT_THREAT_TOLERANCE": 4,
-            "POLICY_MAP_ENF_AUD": {"enforced_id": "audit_id"},
-        }
-
-
-def load_user_config(config_dir: Path) -> dict:
-    user_config_path = config_dir / "user_config.json"
-    if not user_config_path.exists():
-        default_user_config = {
-            "TELEMETRY": "FALSE",
-            "TEXTUAL_THEME": "gruvbox",
-            "EXTRAS": "NOTTODAY",
-        }
-        with open(user_config_path, "w") as f:
-            json.dump(default_user_config, f, indent=4)
-        logging.debug(f"Created user config at {user_config_path}")
-    with open(user_config_path, "r") as f:
-        return json.load(f)
-
-
-def write_config_to_env(config: dict, env_path: Path):
-    for key, value in config.items():
-        if key in PROTECTED_KEYS:
-            continue  # Skip protected keys
-        try:
-            serialized = (
-                json.dumps(value) if isinstance(value, (list, dict)) else str(value)
-            )
-            set_key(env_path, key, serialized)
-        except Exception as e:
-            logging.warning(f"Failed to write {key} to .env: {e}")
-
-
 def setup():
+    """
+    Initialize the application environment:
+    1. Create directory structure
+    2. Load system config (immutable, from system_config.json)
+    3. Load user config (mutable, from user_config.json)
+    4. Configure logging
+    5. Set up .env with WORKING_DIR only
+    """
     base_dir = get_base_directory()
     dirs = {
         "config": base_dir / "config",
@@ -159,20 +117,30 @@ def setup():
         path.mkdir(parents=True, exist_ok=True)
         logging.debug(f"{name.capitalize()} directory ensured at: {path}")
 
+    # Load system config (immutable)
     system_config = load_system_config()
-    configure_logging(dirs["logs"], system_config.get("LOG_LEVEL", "DEBUG"))
 
+    # Configure logging with system-defined log level
+    log_level = get_system_value("LOG_LEVEL", str, "INFO")
+    configure_logging(dirs["logs"], log_level)
+
+    # Load user config (mutable)
+    user_config = load_user_config(dirs["config"])
+
+    # Set up .env file - ONLY for WORKING_DIR (runtime-configurable value)
     env_path = base_dir / ".env"
     if not env_path.exists():
         env_path.touch()
     load_dotenv(dotenv_path=env_path, override=True)
 
+    # Set up working directory (only dynamic value in .env)
     working_dir = Path(os.getenv("WORKING_DIR") or (base_dir / "data"))
     working_dir.mkdir(parents=True, exist_ok=True)
-    set_key(env_path, "WORKING_DIR", str(working_dir))
+    set_key(str(env_path), "WORKING_DIR", str(working_dir))
     os.environ["WORKING_DIR"] = str(working_dir)
     logging.debug(f"Working directory set to: {working_dir}")
 
+    # Create folder structure in working directory
     folders_structure = {
         "Approved": [],
         "Needs_Review": ["Review_First", "Review_Second", "HTML"],
@@ -189,23 +157,4 @@ def setup():
             subfolder_path.mkdir(parents=True, exist_ok=True)
             logging.debug(f" └─ '{subfolder}' subfolder created at: {subfolder_path}")
 
-    user_config = load_user_config(dirs["config"])
-    merged_config = {**system_config, **user_config}
-
-    protected_config = load_protected_config()
-    merged_config.update(protected_config)
-
-    # ✅ URL resolution order: system_config → .env → user prompt
-    url = system_config.get("URL")
-    if not url:
-        url = os.getenv("URL")
-    if not url:
-        url = input(
-            "🌐 Enter the service URL (e.g., https://example.com/api): "
-        ).strip()
-    merged_config["URL"] = url
-    set_key(env_path, "URL", url)
-    os.environ["URL"] = url
-    logging.debug(f"Service URL set to: {url}")
-
-    write_config_to_env(merged_config, env_path)
+    logging.info("✅ Setup complete")