docs: update worktree cleanup docs for pipeline liveness gate [doc-updater]

[james-in-a-box]

Update documentation to reflect changes from 031f08b / #3087:

• docs/architecture/git-isolation.md: Crash Recovery section described orphan detection as a simple container-liveness check. Rewrote the steps and pseudocode to show the new pipeline-anchored check, the fail-safe behavior (sweep skipped if orchestrator unreachable), and the invariant that branches are never deleted by orphan sweeps.
• docs/reference/mcp-deployment-tools.md: prune_stale_worktrees output schema was missing active_pipelines_count. Added it, documented the new 503 response when the orchestrator is unreachable, and noted that worktrees for HITL-parked pipelines are preserved regardless of container liveness.

Triggered by: #3087

Authored-by: egg

[james-in-a-box]

egg is investigating the Test check failure...

• Integration Tests / Integration Tests

[james-in-a-box]

Check Failure: Integration Tests

What's failing: The "Build containers" step of Integration Tests / Integration Tests failed during docker build of the sandbox image. apt-get update could not fetch the deadsnakes PPA index:

W: Failed to fetch https://ppa.launchpadcontent.net/deadsnakes/ppa/ubuntu/dists/jammy/InRelease  503  Service Unavailable [IP: 185.125.189.187 443]
...
#6 ERROR: process "/bin/sh -c apt-get update && apt-get install -y ... add-apt-repository -y ppa:deadsnakes/ppa ..." did not complete successfully: exit code: 100
make[1]: *** [Makefile:542: build-sandbox] Error 1

Root cause: Transient upstream outage at ppa.launchpadcontent.net (Launchpad). This is an external CDN returning 503, not a problem with the build itself.

Why this is not caused by this PR: The PR is docs-only — it modifies docs/architecture/git-isolation.md and docs/reference/mcp-deployment-tools.md, neither of which is referenced by the sandbox Dockerfile or the integration-test build path.

What needs to be done:

• Re-run the failed Integration Tests / Integration Tests job. The autofixer cannot invoke gh run rerun (blocked by the gateway), so a human needs to click "Re-run failed jobs" in the Actions UI.
• If subsequent retries also 503 on the same PPA mirror, consider pinning the apt source or adding a retry loop around add-apt-repository/apt-get update in sandbox/Dockerfile to ride out brief Launchpad outages — but that is a separate hardening change, not something to land on this docs PR.

— Authored by egg

[james-in-a-box]

Autofix tracking

{"Test/Integration Tests / Integration Tests": 1}

[james-in-a-box]

egg check fixer completed for Test. CI will re-run to verify. View run logs

— Authored by egg