Add an option for the submit tool to export a file

[0xba1a]

Reference Issues/PRs

What does this implement/fix? Explain your changes.

As of now the submission tool generates a patch from the git diff. Other than that, if the user wants to get something else from the repo, they can indirectly do it by creating it as a new file in the repo and make it part of the patch.

Instead, this change enables submit tool to handle a file argument. If provided, that file will be simply submitted back to the orchestrator without creating a patch.

[codecov[bot]]

Codecov Report

:x: Patch coverage is 82.95455% with 15 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
sweagent/agent/agents.py	60.86%	9 Missing :warning:
sweagent/run/hooks/apply_patch.py	80.76%	5 Missing :warning:
tests/test_run_single.py	96.77%	1 Missing :warning:

Files with missing lines	Coverage Δ
sweagent/agent/models.py	65.31% <100.00%> (-0.38%)	:arrow_down:
sweagent/tools/tools.py	89.86% <100.00%> (+0.19%)	:arrow_up:
sweagent/types.py	100.00% <100.00%> (ø)
tests/test_run_single.py	97.19% <96.77%> (-0.18%)	:arrow_down:
sweagent/run/hooks/apply_patch.py	76.34% <80.76%> (+1.71%)	:arrow_up:
sweagent/agent/agents.py	67.74% <60.86%> (-0.49%)	:arrow_down:

... and 9 files with indirect coverage changes

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[0xba1a]

It seems that Check Markdown links check failure is not related. It can be addressed in a separate PR.