fatal: not a git repository means Git cannot discover repository metadata from the current directory. For coding agents and automation, that usually signals a broken execution context: the agent started in the wrong workspace, the container mounted only a subdirectory, CI did not check out source, or a worktree path disappeared.

Do not run git init automatically. That can create a new repository inside the wrong directory and hide the real orchestration failure.

Prove the context before acting

pwd
git rev-parse --show-toplevel
git rev-parse --git-dir
git status --short --branch

If rev-parse fails, inspect the workspace supplied to the process. An agent should validate its repository root before reading, editing, staging, or committing files.

Containers and sandboxed agents

Mounting /workspace/src without repository metadata leaves source files but no Git context. Mount the intended working tree and preserve the .git file/directory needed by normal Git commands. With worktrees, .git may be a file pointing into the common repository; do not assume it is always a directory.

Avoid giving a container broad access to unrelated repositories. Give each agent one explicit worktree and verify:

• expected remote URL;
• expected branch or detached-HEAD policy;
• clean/dirty status;
• allowed path scope;
• commit and push permissions.

CI checkout failures

A CI job may run before its checkout step, in a different working directory, or in a later container that did not receive the workspace. Make repository validation an early failing step:

test "$(git rev-parse --is-inside-work-tree)" = "true"
git rev-parse --show-toplevel

Do not discover a missing checkout only after an agent has generated files elsewhere.

Safe recovery

1. Stop the agent or job before it writes further.
2. Confirm the intended repository, branch, and worktree.
3. Restore the checkout or correct the working directory.
4. Re-run status and remote checks.
5. Preserve untracked work before recreating a disposable workspace.
6. Resume from a reviewed state.

The Git foundation covers branches and worktrees. Connect agent execution to Coding Agents, CI checks to GitHub Actions, and failure monitoring to AI Operations.