feat(agent): make multi-repository tasks resumable

[tatoalo]

Problem

Cloud tasks may work across several repositories and branches, while the durable resume checkpoint previously represented only the primary repository.

Why: Multi-repository tasks should resume safely even when a workspace snapshot is unavailable or a feature branch has been deleted remotely.

Changes

• Keep task branch metadata scoped to the primary repository.
• Persist a versioned checkpoint manifest for every repository in the workspace.
• Recreate missing sibling clones and restore their committed, staged, unstaged, and untracked state.
• Keep the primary checkpoint fields compatible with older agents and report incomplete restores honestly.

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Created with PostHog Code

[trunk-io]

😎 Merged successfully - details.

[github-actions]

React Doctor found no issues in the changed files. 🎉

_{Reviewed by React Doctor for commit fad940a.}

[greptile-apps]

Prompt To Fix All With AI

### Issue 1
packages/agent/src/adapters/signed-commit-shared.ts:187
**Primary branch reporting uses path identity**

When an explicit tool `cwd` such as `.` resolves to the primary checkout but the session cwd has a different equivalent representation, the strict string comparison suppresses `reportTaskRunBranch`, causing a later resume to use the wrong or missing branch.

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

_{Reviews (1): Last reviewed commit: "revert(agent): keep cloud resume snapsho..." | Re-trigger Greptile}