Fix multi-file trajectory path handling during save/load

[Aditya-ha11]

Fixes issue where only a single trajectory file path was handled during save/load relativization.

Changes

• Added support for multiple trajectory files using .filenames
• Applied path conversion to all trajectory files instead of just one
• Maintained backward compatibility for single-file trajectories
• Ensured correct handling when reloading via load_new

Notes

• No change to GUI behavior
• Improves API completeness for multi-file trajectories

[Aditya-ha11]

The failing CI checks appear to be due to an external dependency issue with bpy (404 during download), rather than changes in this PR. The error occurs during installation and is consistent across macOS, Ubuntu, and Windows.

Happy to help investigate further if needed.

[BradyAJohnston]

You need tests to check if you are actually fixing what you claim to be fixing.