I am a bit rusty as well with putting back stock stuff on an ox'd system. I guess the first thing I would do since it sounds as if you may not have written down everything you removed is to do a side by side comparison and make a list.
As to getting them back, I know for sure that it would be safest to adb push the stuff to system, and get the permissions correct. You might be able to install the apks, but not sure on that. You can also try just copying them back in place with what ever root file manager you used to remove them, and set the correct permissions. But I will caveat that with again not having done this in a while, you do need to be careful replacing files in the system, while it is running. I am sure some of the less inocuous apps would be ok, but you need to be careful if you hammered away at more of the integrated system apps. There have been a few folks in the D3 forum who have done this, if you do not get additional info here, perhaps IM one of them to see if they can help. I just tend to be very careful right now, as soft bricks are pretty easy to do.
Actually if it were me, I might consider doing nothing, as any OTA does not appear to be immenant, and by the time the first OTA does roll out, there may be other options. If your phone is running correctly, it might be safer. At this point we do not even know for sure what will happen with any OTA's.
I didn't uninstall anything system related. Just stuff like VCast apps, Blockbuster, NFLMobile and some similar stuff.
My phone is running absolutely fine because I didn't uninstall critical apps.
Can there be SBF for the Bionic?
I have very little experience with ADB, unfortunately. Can't I just install the apps and use Root Tools or something to fix permissions?
I also do have a lost of all apk and odex files on a stock Bionic as well as the actual apk files.
I'm fairly confident that I can find which apps I've installed as I didn't uninstall many at all. I just want to rebloat and backup the apps correctly before uninstalling/freezing them again.
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You should be ok then with just applications like that to try and copy them over with your favorite root explorer/file manager program, and set permissions. I have not checked to see what the permissions are in system for these type of files, but you should be able to check other programs and make the new ones match.
As to the SBF, it would surprise me if at some point one does not turn up, but you have to keep in mind that the SBF's are leaks from moto/vzw employees, and come leaked at great risk to the leakee. The tricky part is to make sure any sbf is actually what is either on the phone now, or what will be pushed OTA. The D3 folks had some intermediate SBF's leakes that caused a lot of confusion.
All of the apps which I removed (except for one) were just the .apk file, no .odex file. Those apps installed just fine after using Root Explorer to move them to /system/app.
The last app is VzwDeviceSetup.apk and has .apk file and .odex file. I have the .odex file already in /system/app (it was not deleted when the app was uninstalled). When I try to install the app in Root Explorer it fails, and if I try from adb (adb install r- [path of VzwDeviceSetup.apk]) it fails as well giving the message "Failure [INSTALL_FAILED_DEXPOT]"
Am I correct in assuming I'm having trouble with this app because there's an .odex file associated with it?
Any ideas on how to get this app installed?
Also, how do I set the permissions for the apps which I reinstalled?
Would an app permissions need to be changed if it were a system app but then was reinstalled after being uninstalled?
Can someone verify the permissions for these apps:
Not sure if you still need this, but everything in /system/app appears to be 644 for permissions. Read, checks under owner group and others. Write, check under owner. Execute no check marks. I gave it both ways, depending upon whether your explorer application uses numbers or check marks.
I believe I still need it. Before I made changes, those apps were under applications, but not under the downloaded section, thus uninstallable. Now they're in the downloaded section.
I think they are this was because the permission are wrong.
Do you have any idea about the VzwSetup app and why I cannot uninstall it?
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I am a little confused. The apps that you deleted should be in /system/app. The only download folder I see is in /data/app. The data partition (subdirectory) is where the applications that you download from the market should install. The applications in /system/app would be the ones that came installed on the phone, in this location. If the programs that you reinstalled are in /data/app, then they are not in the original location.
As to your adb "install", I think that it would attempt to install in data. Just a guess here. If I were trying this with adb, I would try and push to system and change permissions from adb, if that is possible. This should be similar to using Root Explorer to move it over, and change permissions. It is just that using Root Explorer on a program integrated into the running OS can be risky or not possible in some cases.
BUT, that file/application has an ominous soundiing name, I would perhaps check in the D3 hack subforum to see if messing with this file would be problematic. If you are trying to uninstall this application from the application menus, it will not uninstall becasue it is part of the Bloat. But I use bloat loosly, as I do not know if this file is more integrated into the OS (soft brick?).
It looks like a custom recovery may be getting pretty close. If this does happen, perhaps some generous soul will create a "stock" backup of the phone (less personal accounts etc.) and make this available for folks who are trying to recreate the stock system. I only mention this, if you are doing anything that you feel uncomfortable about. Having a custom recovery is one step closer to the dev's being able to snag any OTA, root it, and let it out for an install, bypassing a lot of this concern about phones not getting any OTA.
As I mentioned earlier, it might be best to sit tight for a few days, especially if your phone is running correctly. We will have plenty of notice before any OTA is released.