Bump Python to 3.13.11 and uv to 0.9.16

[purplesmoke05]

📌 Description

This pull request updates the project to use Python 3.13 and makes related adjustments throughout the codebase, documentation, and Docker setup. It also updates the uv tool version and improves the formatting and clarity of the documentation in both English and Japanese.

✅ Related Issues

• None

🔄 Changes

Python and tooling version upgrades:

• Updated the required Python version from 3.12 to 3.13 in Dockerfile, tests/Dockerfile_unittest, pyproject.toml, and cmd/explorer/pyproject.toml to ensure consistency across build and runtime environments. [1] [2] [3] [4]
• Upgraded uv tool version from 0.6.5 to 0.9.16 in Dockerfiles to use the latest features and fixes. [1] [2]
• Changed the Python version used by pre-commit hooks to 3.13 in .pre-commit-config.yaml.

Documentation updates:

• Updated references to Python 3.13 in both README.md and README_JA.md, including installation instructions and dependency lists. [1] [2]
• Improved formatting of setup, installation, and usage instructions in both English and Japanese readmes for clarity and consistency (e.g., removing redundant shell prompt symbols, adding code blocks, and clarifying commands). [1] [2] [3] [4] [5] [6]
• Minor formatting and clarity improvements in other sections of the documentation, such as contract versioning, EoL policy, and communication channels. [1] [2] [3] [4] [5] [6] [7]

📌 Checklist

• I have added tests where necessary.
• I have updated the documentation where necessary.

[github-actions]

Coverage Report •

File	Stmts	Miss	Cover	Missing
TOTAL	45571	1590	96%

report-only-changed-files is enabled. No files were changed during this commit :)

Tests	Skipped	Failures	Errors	Time
1529	0 💤	0 ❌	0 🔥	11m 40s ⏱️