Eval cleanup can stop a background server it did not start

[benagentai93-dot]

Baseline

Reproduced from v1.3.1 at 5a306f8956cb1eeae69f9709de0e4d61b44e11e7.

Reproduction

1. Keep a live background server for a project, for example from agents-cli run --start-server.
2. Run local eval generation in the same project.
3. ensure_server() returns ServerInfo(..., started=False), but _run_against_local_server() unconditionally calls stop_server(project_root) in finally.

A deterministic monkeypatch regression supplies a reused ServerInfo and records the cleanup call; the reused server is stopped on both successful and exceptional eval paths. A related replacement race occurs because stop_server() rereads only the current PID file: if the invocation's server was replaced before finally, cleanup can target the replacement.

Actual behavior

Eval can stop a persistent server owned by another invocation. Cleanup identifies only the current project PID metadata, not the process this invocation actually started.

The run command has a sibling failure path: on a local transport error it forces cleanup even for a reused server or a server requested with --start-server.

Expected behavior

Automatic cleanup must run only for a process this invocation started, and only while the current PID metadata still identifies that process. Reused and user-persistent servers must survive success and failure. Explicit agents-cli run --stop-server should remain unconditional.

Minimal fix

Carry the owned PID from ensure_server(); use None for reuse. Pass that PID to a conditional stop_server(expected_pid=...) seam. Preserve the original --start-server cleanup decision across transport errors. No new dependency or lifecycle abstraction is needed.

Reference implementation: benagentai93-dot@b4646e6

Test evidence

Runnable regressions cover eval success/error with owned/reused servers, run success/error with and without --start-server, replacement PID refusal, and explicit stop behavior.

Fork verification:

• focused lifecycle suite: 22 passed
• full root suite: 41 passed
• ruff check src tests: passed
• ty check src: passed
• uv build: passed
• installed-wheel agents-cli --version: 1.3.1 on Python 3.11 and 3.13