Multi-repository environments serialize on one lease slot and cannot set up checkouts

[danny-avila]

A common trusted-VM layout is one environment whose root holds several checkouts (for example root: /home/<user>/src containing LibreChat, agents and code-interpreter). With that layout:

• All work serializes. Workspace lease slots only parallelize distinct registered roots, so raising LIBRECHAT_CODE_WORKSPACE_LEASE_SLOTS does nothing for one broad root. On one deployment with a single broad root, 10-31% of execute_command requests per day hit the 30 s WORKSPACE_QUEUE_TIMEOUT (1,775 of 5,744 on the busiest day). Agents that start background checks in parallel only queue them.
• No per-checkout setup. setup runs at worker start with cwd at the root, and per conversation worktree only when --conversation-worktree-root is set and the sources are git repositories. actions always run with cwd forced to the root. Nothing can run a repository's own bootstrap (for LibreChat, npm run smart-reinstall) in a fresh worktree of one of the contained checkouts, so agents improvise, for example by symlinking another checkout's node_modules, which resolves workspace packages to the wrong branch.
• Credentials: with checkout routing, the broad root is not itself a repository, so actions and setup at the root get no GitHub credentials.

Environments cannot overlap, so a per-repository environment cannot sit beside the broad one.

Proposal

Allow an environment to declare repositories inside its root, each with its own setup and lease capacity. Sketch:

name: primary
root: /home/ubuntu/src
repositories:
  - path: LibreChat
    setup: { command: npm run smart-reinstall -- --skip-client, timeoutMs: 900000 }
  - path: agents
    setup: { command: npm ci, timeoutMs: 600000 }

• Each repository (and each conversation worktree created from it) is its own lease key, so work in different repositories runs in parallel up to the negotiated slot count.
• setup runs once per new worktree of that repository, with cwd at the worktree and that repository's credentials.
• Alternatively, allow non-overlapping child environments under a parent root.

Acceptance

• Two commands in two different repositories of one environment run concurrently with 2 slots.
• Creating a worktree of LibreChat runs its declared setup there, with LibreChat-scoped credentials.
• Existing single-root environment definitions keep working unchanged.