How do I get to that file directory and extract them?
You can use Internals Pro from Preware
Alternatively you can use WinRAR, 7ZIP or another tool to open the Doctor.jar file. Go to the "Resources" folder, you should find webOS.tar in there, open this and you should find a "rootfs" tar.gz inside of webOS.tar. For the "Unlocked Pre 3" this is called "nova-cust-image-mantaray-rootfs.tar.gz"
Inside the rootfs.tar.gz you have the whole file structure, so you can go to usr\palm\applications