Enhance user configuration management and logging

- Introduced user configuration command to set API key.
- Updated README and documentation for user config and logging paths.
- Refactored logging to support user-specific log files.
- Added tests for user configuration and logging behavior.

tests/test_logging_config.py

@@ -1,8 +1,9 @@
 from __future__ import annotations
 
 import logging
+from pathlib import Path
 
-from nexus_claude_api.logging_config import configure_logging
+from nexus_claude_api.logging_config import configure_logging, resolve_log_file
 
 
 def test_configure_logging_writes_app_logs_to_file_without_console(
@@ -55,3 +56,17 @@ def test_configure_logging_verbose_writes_debug_app_logs_to_file(
         app_logger.handlers.extend(original_handlers)
         app_logger.setLevel(original_level)
         app_logger.propagate = original_propagate
+
+
+def test_resolve_log_file_uses_user_config_dir_by_default(
+    tmp_path,
+    monkeypatch,
+) -> None:
+    user_config_dir = tmp_path / ".config" / "nexus-claude-api"
+    monkeypatch.setattr("nexus_claude_api.config.USER_CONFIG_DIR", user_config_dir)
+
+    assert resolve_log_file() == user_config_dir / "logs" / "nexus-claude-api.log"
+
+
+def test_resolve_log_file_uses_local_logs_in_dev_mode() -> None:
+    assert resolve_log_file(dev=True) == Path("logs") / "nexus-claude-api.log"