Apply TODO.md template tasks (uv tasks, git-cliff default, logging consolidation, bump_version move, no empty files)

[buddingengineers12345]

Summary

Implements all items from TODO.md:

• Remove uv self update from Copier post-gen tasks.
• Default include_git_cliff to true.
• Move generated bump_version.py into src/{{ package_name }}/common/ and update the release workflow + _skip_if_exists sync.
• Remove logging_config.py / include_logging_setup in favor of common/logging_manager.
• Prevent empty optional files by using conditional template filenames for CLI, docs, and git-cliff artifacts.

Maintenance

• Merge conflict resolution: rebased by merging latest main into the branch and resolving conflicts in copier.yml, scripts/sync_skip_if_exists.py, and tests/test_template.py.

CI

• just ci