What's the point with adding support to vp's? If you use this app, it means you're developing a mod or at least messing with the modpack, which again means you've already extracted contents of vp-files. Even if you run this app against vp-files, you're not going to be able to do any cleaning unless you extract said vp-files. It seems a lot of work for no gain whatsoever to add support for vp's.
Which is the case for weapon_expl.tbl (according to the Wiki), so at least that should be alright.
Well, if may want to consider adding a notification that weapon_expl.tbl references to unused effect and it could be removed from tbl as well as the effect itself.
Cleaning other folders, I dunno. Maps and effects are the usual memory hogs, and AFAIK there's no real challenge in the other folders (it's all used in the same way as maps and effects) so at that point it just becomes cumbersome and repetitive, not much of an exercise anymore.
Memory hogs yes, but I think this tool has real potential to become a true modpack cleaner and it'd be real benefit to everybody to not bundle useless files in their modpacks. A lot of mods these days have a ton of files in their interface folder for example, which makes noticing unused files hard.
How about setting up svn repository for this, it'd be a lot more convenient for people to contribute? That way you don't have to add features that have no interest to you, but others may want to. And everyone benefits from it.