[misc] chore: sync latest code base

[yyDing1]

Summary

Minor data-pipeline / eval fixes and housekeeping for the SWE-agent examples.

Data preprocessing

• swe_rebench.py: add a SKIP_INSTANCES hook and drop instances without an image; remove the git checkout <base_commit> / git clean steps from the per-instance reset; print the final instance count.
• swe_rebench_v2.py: filter out instances whose deployment image is None.

Eval / reward

• reward/swe_rebench.py: skip the test-file reset when a task has no modified test files (avoids running git checkout <commit> with no paths).

Agent loop

• agent_loop.py: move the per-run log handler and config logging inside the concurrency semaphore.

Misc

• run_infer.sh: point the example at the modal parquet/config and bump --nnodes + sampling params.
• README.md: add supervisor note to the citation.
• Bump the verl submodule.

[gemini-code-assist]

Code Review

This pull request updates data preprocessing scripts for SWE-rebench, adjusts agent interaction parameters in run_infer.sh, moves logging initialization inside the semaphore block in agent_loop.py, and adds a safety check for empty test files in swe_rebench.py rewards. The review feedback suggests two improvements: defensively creating the output directory in agent_loop.py to avoid a potential FileNotFoundError before adding the file handler, and using shlex.quote and -- in git checkout within swe_rebench.py to prevent shell injection and option parsing issues.

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[gemini-code-assist]

To prevent potential shell injection vulnerabilities or command execution failures, filenames should be properly escaped using shlex.quote when constructing shell commands. Additionally, using -- before the file list in git checkout is a best practice to prevent filenames starting with a dash (-) from being interpreted as command-line options.

Suggested change

	if test_files:
	reset_tests_command = f"git checkout {base_commit} {' '.join(test_files)}"
	else:
	reset_tests_command = "echo 'skip reset'"
	if test_files:
	import shlex
	reset_tests_command = f"git checkout {base_commit} -- {' '.join(shlex.quote(f) for f in test_files)}"
	else:
	reset_tests_command = "echo 'skip reset'"

[gemini-code-assist]

The directory self.output_dir is not guaranteed to exist when add_file_handler is called. If the logging handler tries to open the log file before the directory is created, it can raise a FileNotFoundError. Creating the directory defensively before adding the file handler prevents this potential failure.

Suggested change

	add_file_handler(self.output_dir / "run.log", self.run_id)
	self.output_dir.mkdir(parents=True, exist_ok=True)
	add_file_handler(self.output_dir / "run.log", self.run_id)