Refine PyPI packaging and source distribution contents

[davidkfoss]

Summary

This PR cleans up the packaging configuration for pulseopt and clarifies how repository examples are distributed and used.

Changes

• Add MANIFEST.in to control source distribution contents.
• Exclude local development files and build artifacts from the PyPI source distribution.
• Include runnable example scripts in the source distribution.
• Keep examples out of the wheel so normal installs remain minimal.
• Update README wording around examples, PyPI source distribution, and repository layout.
• Update pytest configuration for the src/ layout.
• Update stale tests to match the current context logging schema.

Packaging behavior

Expected artifact split:

• sdist: includes source files, tests, and examples.
• wheel: includes only the installable pulseopt package and metadata.
• development files such as uv.lock, .python-version, .venv, caches, and CI metadata are excluded from published artifacts where appropriate.

Validation

• uv build
• uv run pytest
• uv run ruff check .
• Verified that examples are included in the source distribution.
• Verified that examples are not included in the wheel.