Fix command prefix bug

[cynthia-d-lo]

Currently, if a user specifies a custom command prefix and the project directory does not match the source directory, we append --project <project dir> to the command prefix regardless of whether command-prefix is a uv command.

This pr ensures that the --project flag is only appended to uv commands.

[github-actions]

📖 Docs preview: https://smokeshow.helpmanual.io/0i4j5v393y5q5a173z2l/

[Copilot]

Pull request overview

This PR adjusts how submit_to_aml() constructs the runtime command so that --project <dir> is only appended when the user’s command_prefix is a uv command, avoiding incorrect flag injection for non-uv prefixes when project_dir != source_dir.

Changes:

• Gate the --project <relative dir> append behind a command_prefix uv-prefix check.
• Keep existing behavior of computing the project path relative to source_dir for the job’s runtime command.

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[cynthia-d-lo]

Following

submit-aml/src/submit_aml/command.py

Lines 96 to 98 in 880c293

	if command_prefix.startswith("uv run"):
	logger.info('Adding debugpy to uv run command using "--with"')
	command_prefix += " --with debugpy"

, I decided to narrow the check to .startswith("uv run")` in 675e038

I contemplated adding a use_uv flag instead, but I decided against it because it created a confusing user experience (users would always have to remember to unset use_uv when using a non-uv command_prefix).