Restore validated safety behaviour and prepare v0.1.1

[RhysWhite]

Summary

This pull request synchronizes the public NEXCISION source with the implementation used in the formal validation and prepares the v0.1.1 patch release.

Safety behaviour restored

• Prevents accidental removal of every matrix row unless --allow-empty is explicitly supplied.
• Stages requested outputs before committing them and rolls back partial writes if a multi-output operation fails.
• Handles invalid UTF-8 input files with controlled errors.
• Records the allow_empty setting in the JSON provenance report.
• Adds regression tests covering these behaviours.

Release preparation

• Bumps the package version to 0.1.1.
• Updates release and citation metadata.
• Adds a detailed plain-English code walkthrough and links it from the README.

Validation

All tests pass:

Ran 26 tests — OK