Refactor, Documentation, and Code Cleanup (#70)

Code Quality:
- Add markdownlint to pre-commit hooks for consistent markdown formatting
- Add missing type hints to constants and variables
- Prefix helper functions with underscore for better encapsulation

Documentation:
- Update README.md to follow markdown best practices
- Add docstrings to functions in process_query.py, server_utils.py and main.py

Refactoring:
- Remove redundant normalize_pattern function from client.py
- Simplify logic in should_exclude function in ingest_from_query.py
- Improve code organization in clone.py
- Move async_timeout comment into function body for better context

.pre-commit-config.yaml

@@ -76,3 +76,10 @@ repos:
     rev: v1.36.4
     hooks:
       - id: djlint-reformat-jinja
+
+  - repo: https://github.com/igorshubovych/markdownlint-cli
+    rev: v0.43.0
+    hooks:
+      - id: markdownlint
+        description: "Lint markdown files."
+        args: ["--disable=line-length"]