[Kyocera Zio M6000] pomeroythomas:
Okay. I don't have a lot of knowledge on developing/tinkering on Android, but I think I've figured out how to integrate apps into the ROM (updates of system apps and/or downloaded apps). I used:

A stock cricKet 2.2.1 ROM, rooted (of course) w/Universal Androot

Root Explorer, and

ROM Manager (more on this later)

First thing is first, I did a TI backup; don't want to lose anything

I then opened Root Explorer

Mounted R/W, and

did a search for .apk.

Notice that the only directories the actual .apk files for INSTALLED apps should appear in (outside the SD card) are:

/cache

/data/app

/data/app-private (possibly)

/data/FLEX/app

/system/app

Ignore the following:

/cache

/data/FLEX/app

Now, you may already know this, but the system apps you're looking for are located in the /system/app directory, and downloaded apps (for the updated system apps) are located the /data/app directories that aren't being currently ignored (if you're following my instructions). Based on icon, filename, and common sense, I found which .apk files were the updates of already existing system apps (IE Market, Google Maps, Voice Search, etc.) in the /data/app directory, and the corresponding system app they updated in the /system/app directory. I then:

Copied the filename of the system app I was going to replace (rename copy all)

Moved over to the /data/app directory

Located the corresponding updated app

Renamed it what its corresponding system app was renamed (rename, delete existing name, paste)

Hit the 'move' option

Navigated to the /system/app directory

Deleted original system app (you may want to backup this file beforehand)

Pasted the updated system app

Within 30 seconds or so, you should get a (blah.blah.blah has unexpectedly shut down force close/report) popup. Just hit force close and you should be fine (Google Maps seemed to be a recurring FC). If you try to open the app before rebooting, it will force close on you. When you're finished, open ROM Manager. I know you're thinking 'This app is no good on the ZIO'; so stop. Hit 'Fix Permissions'. The reason for this is that it fixes a few rare force close issues. I don't know the mechanics of it, but it works, so I don't question it. Listen to the notification you'll see and reboot your phone after it finishes fixing the permissions. Now go into settings and manage applications, and you'll see that you can no longer uninstall whatever apps you moved to the /system/app directory.

FYI Renaming .apk files doesn't seem to make a bit of difference either way.

(Forgive my horrible perspective descriptions: I/you)

I haven't tested it yet, but I believe unrooting the device should make any apps moved to the /system/app directory that require root access would become non-functional (right?). The reason this thread is a question is that I'm wondering if i did this correctly, and if so, I want to find out if unrooting and factory resetting my phone would somehow delete the apps in the /system/app directory that weren't included in the stock ROM. (I'm not really willing to do that yet; I still have to download the SDK to my new computer so I can do a NANDROID backup.) Any help answering these from a more experienced developer would be great.