Firstly, I suggest anyone who wants to mod TF3D/Manila/Sense gets
"CFC GUI".
Watch little sample Youtube video
here...
Also, you forgot about XML's, PNG's, & HTML's.
LUA's are script, they descript the animations & actions of the page, as well as the Landscape Layout. (They need to be dumped before editing & re-compiled afterwards. Not for the unexperienced)
Mode9's are a specail xml layout format, similiar to how Titanium uses CPR's. It lists which files to use & they layout. (Need Mode9 editor to edit these. They can take some time to figure out, not for the unexperienced)
XML's are the text being used by the tab, you'll notice they have different copies for each language.
PNG's are obviousely Images like the QTC's
QTC is an ATI 3D texture formate as Qualcomm CPU's use an ATI graphic chip. (NOTE: AMD sold the mobile chip devision to Qualcomm when they merged)
HTML's are "About" files that most apps use.