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Agent Instructions

This repository's operating protocol lives in .session.md.

Before doing substantive work, read .session.md in full and follow it. It covers startup context loading, session setup, session lifecycle, skill loading, Worktrunk branching, session journaling, file schemas, architecture, and process expectations.

If .session.md is missing, stop and tell the user the session protocol is not installed correctly.

Sub-repository workflow

This is a meta repository. Directories cloned by init.sh, including networking/, aws/, and agentcompute/, are independent Git repositories. They are ignored here and are not submodules.

For work inside a sub-repository:

  1. Treat the sub-repository as the repository root. Do not create its implementation branch or worktree from this meta repository.
  2. Before editing, run git fetch origin --prune and wt list --format=json in the sub-repository.
  3. Create a unique implementation branch and Worktrunk worktree from the fetched default branch. Use wt switch --create --base origin/<default-branch> --no-cd --format=json <branch> and work only in the returned path.
  4. Run validation, commit, and push from that sub-repository worktree. Integrate through a GitHub pull request with squash merge unless the user explicitly requests a direct default-branch commit.
  5. Do not use wt merge, wt step push, or local git merge as the default integration path. Remove the implementation worktree with wt remove after integration.
  6. Never stage cloned sub-repository contents in this meta repository and never convert them to Git submodules.

Documentation workflow

For documentation work in this meta repository or any cloned sub-repository, read and follow .agents/skills/gilmanlab-documentation/SKILL.md from the meta repository root. Its document classification, ownership rules, lifecycle, and decision and design templates are required. Keep this skill canonical in the meta repository; do not copy it into each sub-repository.

All GilmanLab documentation is centralized in this repository under docs/. Sub-repositories must not create their own docs/ trees; a documentation change motivated by sub-repository work is a companion change in this repository. When a sub-repository change alters behavior that is documented here, update the affected documents in the same unit of work.

Build and verify the site with moon run docs:build before merging documentation changes.