A conflict run that finds the work already done closes the pull: no conflict loops #2125

A conflicted pull whose work is already on main now closes as superseded, so it can't loop through conflict runs again.

I ran test/conflict_sweep.test.ts (7 pass), the other conflict, already-done and autonomy tests (45 pass in total) and tsc --noEmit (clean). I did not run the whole suite; a full bun test timed out here.

What changed, all in src/crew/autonomy.ts:

• No change left: when the sweep merges main into a pull and the resulting tree equals main's own tree, it closes the pull without queueing a run. It comments, naming the main tip that carries the change, and closes the issues named in "Closes #N" as done.
• Run says "already done": a run that ends already done: <oids> on a pull now closes that pull the same way, naming those commits. This is closeSuperseded, called from settleAgentRun. Before, only a plain issue got a note and the pull stayed open.
• Cap per main tip: the sweep queues at most two conflict runs for a pull for the same main tip. The count lives in memory, so a restart resets it. Persisting it would need a column on the run.

I changed two existing tests, because the old versions were wrong. They simulated a builder "bringing the branch level" by writing the branch identical to main. Under the new rule that pull adds nothing, so it correctly closes. Each branch now also adds a file of its own.

New tests:

• A pull already carried by main is closed on the first pass with zero runs.
• A run answering already done closes the pull and its issue.
• The same main tip asks the crew at most twice.

I added no dependencies.

Closes #2121