Add file.flush() call in append_entry() to ensure planner history
entries are written to disk before git commits execute. While the
file handle drop should flush, explicit flush simplifies reasoning
about the ordering invariant.
Extend code comments in stage_and_commit() to document that the
write_git_commit-before-git::commit ordering has regressed multiple
times and must be preserved in any refactoring.
Requirements: completed_requirements_2025-12-11_10-05-08.md
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