chore: update logging configuration and enhance project structure

- Added new logging configuration to improve observability across various services.
- Introduced a `.repomixignore` file to exclude unnecessary files from version control.
- Updated `pyproject.toml` to include additional paths for script discovery.
- Refreshed submodule references for the client to ensure compatibility with recent changes.

All quality checks pass.

repomix.config.json

@@ -12,9 +12,9 @@
     "files": true,
     "removeComments": true,
     "removeEmptyLines": true,
-    "compress": true,
+    "compress": false,
     "topFilesLength": 5,
-    "showLineNumbers": false,
+    "showLineNumbers": true,
     "truncateBase64": false,
     "copyToClipboard": false,
     "tokenCountTree": false,
@@ -26,11 +26,67 @@
       "includeLogsCount": 50
     }
   },
-  "include": ["src/"],
+  "include": [
+    "tests/quality"
+  ],
   "ignore": {
     "useGitignore": true,
     "useDefaultPatterns": true,
-    "customPatterns": []
+    "customPatterns": [
+      "**/*_pb2.py",
+      "**/*_pb2_grpc.py",
+      "**/*.pb2.py",
+      "**/*.pb2_grpc.py",
+      "**/*.pyi",
+      "**/noteflow.rs",
+      "**/noteflow_pb2.py",
+      "src/noteflow_pb2.py",
+      "client/src-tauri/src/grpc/noteflow.rs",
+      "src/noteflow/grpc/proto/noteflow_pb2.py",
+      "src/noteflow/grpc/proto/noteflow_pb2_grpc.py",
+      "src/noteflow/grpc/proto/noteflow_pb2.pyi",
+      "**/node_modules/**",
+      "**/target/**",
+      "**/gen/**",
+      "**/__pycache__/**",
+      "**/*.pyc",
+      "**/.pytest_cache/**",
+      "**/.mypy_cache/**",
+      "**/.ruff_cache/**",
+      "**/dist/**",
+      "**/build/**",
+      "**/.vite/**",
+      "**/coverage/**",
+      "**/htmlcov/**",
+      "**/playwright-report/**",
+      "**/test-results/**",
+      "uv.lock",
+      "**/Cargo.lock",
+      "**/package-lock.json",
+      "**/bun.lockb",
+      "**/yarn.lock",
+      "**/*.lock",
+      "**/*.lockb",
+      "**/*.png",
+      "**/*.jpg",
+      "**/*.jpeg",
+      "**/*.gif",
+      "**/*.ico",
+      "**/*.svg",
+      "**/*.icns",
+      "**/*.webp",
+      "**/*.xml",
+      "**/icons/**",
+      "**/public/**",
+      "client/app-icon.png",
+      "**/*.md",
+      ".benchmarks/**",
+      "noteflow-api-spec.json",
+      "scratch.md",
+      "repomix-output.md",
+      "**/logs/**",
+      "**/status_line.json"
+    ]
   },
   "security": {
     "enableSecurityCheck": true