Agent instructions

Workflow

Flow: run-github-coding-agent-runner.sh → container → start.sh → Actions listener.

Standalone: run ./run-github-coding-agent-runner.sh with required flags (--github-token, --github-repository, --script-dir, --runner-base). No env needed.
SLURM: set GITHUB_TOKEN and GITHUB_REPOSITORY, then sbatch run-github-coding-agent-runner.sh. When the script runs under SLURM with no arguments, it uses env and SLURM defaults (SLURM_SUBMIT_DIR, WORK) for script-dir and runner-base. start.sh installs/configures the runner in RUNNER_HOME if needed and starts the Actions listener; workflow jobs run in the container.

When editing scripts or config in this project:

Never add sensitive data to scripts or committed files.
Do not hardcode tokens, passwords, API keys, or other secrets. Use environment variables or a secure mechanism outside the repo (e.g. export GITHUB_TOKEN before running).
Never use host-specific absolute paths.
Do not add paths like /work1/amd/josantos/... or other machine-specific directories. Prefer:
- Paths relative to the script (e.g. SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)" then cd "${SCRIPT_DIR}").
- Environment variables (e.g. $WORK, $HOME) when a base directory is needed.
- Relative paths from the project or script location.
Never edit the container definition file (e.g. iris.def) unless explicitly asked.
Prefer changing scripts (e.g. start.sh, run-github-coding-agent-runner.sh) to install, configure, or run things at runtime. Only modify .def files when the user explicitly requests it.