chore(deps): update Python dependencies and fix security vulnerabilities

- Fix urllib3 decompression bomb vulnerability (CVE in v2.6.2)
- Fix filelock TOCTOU race condition vulnerabilities (CVE in v3.20.2)
- Update docling 2.66.0 -> 2.68.0
- Update transformers 4.57.3 -> 4.57.6
- Update numpy, scipy, opencv-python and other dependencies
- Remove unused tree-sitter-java

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: bundolee