MISSING FILES?

Me and my team are working on a game, and we just finished our system test and getting ready for creating a demo. However when making the game I came across some odd occurrences.
To start off, this is what it looks like when I run the RPG2003:


Nice and normal, still a WIP, right? For some odd reason when I go to the actual folder in the system every file that contains, sprites, facesets, etc. is blank! Nothing is there besides one prototype chipset set from forever ago when I ran the program as administrator to create the project. I was thinking that might have been the problem and I should have probably ran the program as administrator always. However, I have a external hard-drive and I'd like to put the project in the hard-drive so I have backup just in case my computer goes wacko on me again but when I transfer the file it's the version of the games prototype from like forever ago and I'm so confused and a little worried. Please someone help me out here. Thanks in advance.

Yes!

The standard RTP folder has all the defaults in each folder but the folder in the projects folder named Test2 contains nothing but empty folders and a chipset folder from forever go that is currently not being used.

author=PepsiOtaku
That's normal. You have to add the resources you use to your folders manually, or package your RTP when you go to "Create Gamedisk" from the file menu. I recommend the former though as it means smaller filesize. There's a great tool appropriately called "RMTool" that will move all the resources you are using automatically into your project folder. You shouldn't really have to use "Create Gamedisk"

You should be able to download it from here:
http://rpgmakertimes-companion.blogspot.com/2010/03/rmtool.html

That worked! Thanks so much!