Validate generated outputs against a manifest

[aaronsky]

Description

Stacked on #360.

Adds --expected-output-manifest so Stone can compare generated output paths against a checked manifest.

Checklist

General Contributing

• Have you read the Code of Conduct and signed the CLA?

Is This a Code Change?

• Non-code related change (markdown/git settings etc)
• Code Change
• Example/Test Code Change

Validation

• Have you ran tox?
• Do the tests pass?

Verification run directly with the CI lint/test steps:

• uv run --no-project --with-requirements requirements.txt --with-requirements test/requirements.txt --with flake8==5.0.4 --with pylint flake8 setup.py example stone test
• uv run --no-project --with-requirements requirements.txt --with-requirements test/requirements.txt --with flake8==5.0.4 --with pylint --with setuptools pylint --rcfile=.pylintrc setup.py example stone test
• uv run --no-project --with-requirements requirements.txt --with-requirements test/requirements.txt --with pytest --with mock pytest
• uv run --no-project --with-requirements requirements.txt --with-requirements test/requirements.txt --with enum34 --with mypy --with types-six ./mypy-run.sh

[CLAassistant]

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2 out of 3 committers have signed the CLA.

✅ musicinmybrain
✅ aaronsky
❌ rhui-dbx
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