V2 Released

Changelog:

• moving objects to a hidden scene (showing all hidden objects wasn't ideal)
• applied objects will be inside the originals collection instead of it's own keeping the outliner clean
• objects will maintain relationships to other objects
• there's an indicator across the bottom of the screen that lets you know from a glance whether you are working with an applied object or original
• weight paints / uv maps and materials will be retained across applied objects so you can still do edits to your applied objects the only changes are geometry differences if you edit your original.

Notes:

• Some funkiness can occur if you add or delete faces / edge loops, with weights and possibly uvs when making changes to your original object.  In which case it's best to unwrap your model again, bake again and weight it again.  Otherwise if you just want to tweak vertices everything should be smooth. (edited)