Add AST caching and optimized module usage checks in DependencyExtractor

- Introduced caching for AST file data and dependency check results to improve performance.
- Enhanced the `is_module_used_in_ast` and `batch_check_modules_usage` functions to utilize caching.
- Updated the `extract_dependencies_from_cmt_info` function to support batch filtering of dependencies based on AST data.
- Simplified AST file path resolution and reading logic for efficiency.
- Added handling to skip incremental directories during file scans.

Author: mununki