fix(agent): shallow clone repositories for cloud tasks

[tatoalo]

Problem

Repository-less cloud tasks need to discover and clone the right repository at runtime. A normal clone can download years of history and tags for large repositories, and Auto mode paused for approval before the new repository tools could run.

Changes

• expose local repository listing and cloning tools to repo-less Claude and Codex cloud sessions
• clone with a single branch, depth 1, and no tags through the existing clone saga
• tell the agent to use the repository tools and deepen history only when needed
• allow the trusted local repository setup tools to run without a permission prompt in Auto mode

[trunk-io]

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[github-actions]

React Doctor found no issues in the changed files. 🎉

_{Reviewed by React Doctor for commit 6380d23.}

[greptile-apps]

Prompt To Fix All With AI

### Issue 1
packages/agent/src/adapters/local-tools/tools/clone-repo.ts:114
**Shallow clone breaks branch switching**

When `clone_repo` is called again for a different branch of the same repository, the existing-clone path runs `checkout(branch)` without fetching it, but the initial `--single-branch` clone has no ref for that branch, causing the checkout to fail and leaving the agent on the previously cloned branch.

---

For each issue above, determine whether it is valid and should be fixed. If so, fix it directly.

_{Reviews (1): Last reviewed commit: "fix(agent): allow repository setup in au..." | Re-trigger Greptile}

[veria-ai]

High: GitHub token becomes readable by the agent

Enabling channelMode exposes clone_repo, which clones using a URL containing the GitHub token. Git saves that URL as remote.origin.url in .git/config, so a malicious task can call clone_repo and then read the current token from the cloned repository. Authenticate through a temporary credential helper or HTTP authorization header instead, and ensure the stored origin URL never contains credentials.

[veria-ai]

PR overview

This pull request changes the agent’s cloud-task repository cloning behavior to use shallow Git clones, including cloning through the Claude agent’s clone_repo capability.

One high-impact issue remains open: when channel mode is enabled, a task can clone a repository and then read the GitHub token persisted in the clone’s Git configuration. This exposes a live credential to potentially malicious agent workloads and should be fixed by using non-persistent authentication before merging.

Open issues (1)

• High: GitHub token becomes readable by the agent — packages/agent/src/adapters/claude/claude-agent.ts:2000

Fixed/addressed: 0 · PR risk: 8/10