Themes is for the old xpfe way of doing things. Toolkit is the Aviary way. Also, apparently there are theme-specific (classic and modern for xpfe, pinstripe and qute for aviary) icons for each.
I believe (without much evidence) that lxr only indexes files whose first n bytes are in the ASCII range. I don't know what the value of n is, but apart from .png files I know that it doesn't index files that begin with a BOM
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Themes is for the old xpfe way of doing things. Toolkit is the Aviary way. Also, apparently there are theme-specific (classic and modern for xpfe, pinstripe and qute for aviary) icons for each.

As for resizer being missing: ask on #bmo
lxr.mozilla.org/mozilla1....
lxr.mozilla.org/mozilla1....
For that matter, why are thousands of .gif and no .png files found?
There's also version.txt that is missing - it's supposed to be right by the mozconfig in each of the toolkit apps.
I'd bet on lxr not indexing .png files...
I believe (without much evidence) that lxr only indexes files whose first n bytes are in the ASCII range. I don't know what the value of n is, but apart from .png files I know that it doesn't index files that begin with a BOM