The problem why TexturePacker does not write PVRTC for spine / libgdx is that I don't know what to write in the "format" field of the .atlas file....
I did not see any definition for PVRTC in the Java definitions. Maybe there are some newer values I did not know about when we created the exporter?

Well... linux... I really wanted to support it but since not even 2% of the users are linux users...
I plan to release an 3.x.x versions if I find the time - but I don't call it a fully supported platform.

TexturePacker(Pro) supports folders if you add complete folders instead of individual images.
It just removes the top folder.

@YaW - just add your "images" folder from the screenshot above.
The paths should be available now.

Paths are removed if individual sprites are used.