- Do not ask whether to create a git commit or push after making changes.
- When the user says "commit and push", immediately run the necessary git commands (including
git add,git status,git commit,git push) without any further confirmation or questions. - Never ask whether to run
git commitorgit pushafter the user has already said "commit and push". - For Snakemake runs, use a longer command timeout to avoid premature termination.
- Never commit or push SLURM output files (e.g.,
slurm-*.out) or Snakemake log files (e.g.,*.snakemake.log,.snakemake/log/*).