agent: save the proof tree with the run's other outputs

[dingf3ng]

Supersedes #16, which fixed the same problem the wrong way: it deleted the proof tree files instead of moving them.

The problem

ProofController._finish_proof writes <theorem>_proof_tree_final.png and .json next to the file being proved. That is the wrong directory. The tree is a run artifact, and every other run artifact — autorocq.log, the resulting .v — already goes to the output directory main.py builds for the run.

Consequence:

• Named after the theorem rather than the run, each run overwrites the previous run's tree.

#16 deleted the files during cleanup. That removes the litter but throws the tree away: nothing else persists it — ProofRecorder writes statistics, never the tree — so those two files were the only copy.

The change

ProofController takes the run's output directory, and _finish_proof writes the tree there. main() records the resolved directory on the config, the way it already does for config.log_file, so initialize_components can pass it down.

A None default keeps the old behaviour for callers with no run directory. Each test that builds a controller now passes the directory its own run already owns — results_dir for the batch test, the temp copy's directory for the rest.

utils/scratch.py is untouched: with nothing landing in the source tree, there is nothing to clean up.

Checking

Drove _finish_proof both ways on a temporary tree:

	run dir	source dir
output_dir set	my_thm_proof_tree_final.{json,png}	empty
output_dir=None	—	falls back beside the .v, as before