Add apply_transform pipeline for moving images and channels

[zh320]

This PR adds support for applying transforms to moving images and channels after point-set registration.

This PR depends on PR #36.

Updated workflow

• Apply transforms to moving images using parameter maps from point-set registration.
• Support multiple moving inputs and channels in apply_transform.
• Extend snakefile and tests for apply_transform workflows.

Additional updates include config cleanup, output path consistency improvements, and updates to reference test data.