here's a note about what i posted:

it leaves permissions set to the actual php script that you ran, so you need to change permissions with these commands, i'm not 100% sure what you should do.
use:
umask
chgrp
chmod

it seems as though when i did a chmod -R 777 and a chgrp -R WWW that i was able to erase things, modify them, and chmod them like normal.

the normal chmod command only changes one single file or folder; it doesn't modify contents of a folder. the workaround for this is to use the -R tag, i did a shell_exec("chmod -R 777 Path/To/Dir"); since I don't know how i would do that with the normal php chmod command.

i've been working on this for a while now, I think I have more of an idea of how to do all of these. I've successfully been able to extract zip files and gzips (.tar.gz). do a google search for the unix versions of these commands as well as the php versions, it helped me a lot and it could help you too.
tell me if you know of any more.