Here is a good directory structure you can use to manage your thesis.
Thesis (Maya project root)
/Images - renders and playblasts
-->/shot01
---->/playblasts
---->/renders
/Scenes
/Animation - do character and fx anim here
/Layout (these can be broken down into scenes as well)
animatic.mb (cameras are setup here)
/Production (these files are broken
/scn01_rooftop
/scn02_heaven
scn02_heaven_BLK_01.mb
scn02_heaven_1STpass_03.mb
scn02_heaven_FINAL_02.mb
/Assets - your assets
/Characters
/Damien
damien.mb
/Sets
/rooftop
/Props
/Rendering - do your lighting here
/scn01
/scn02
Textures can either be stored inside each model's directory as a subfolder, or in the sourceImages folder.
Assets are referenced into animation, animations are referenced into rendering.
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