[codex] harden writes and semantic timeline diffs

[explicit09]

Summary

• harden repository ref/object writes with atomic file replacement and related checks
• preserve richer OTIO effect identity, including effect_name, in semantic diff payloads
• report transition changes only when the transition remains between the same adjacent clips
• update CLI/Python rendering/tests and architecture docs for the richer diff contract

Validation

• cargo fmt --check
• cargo test -p vedit-core
• cargo test -p vedit-cli
• cargo test -p vedit-py
• uv run --project crates/vedit-py --with pytest python -m pytest crates/vedit-py/tests/test_workflow.py