[Samsung Galaxy Nexus] bishop41466:
Before I ask questions, thanks to efrant for your awesome instructions! They worked like a charm!

I am on JB right now, but some data on the phone seems to be corrupted or have wrong ownership/permission. Currently, the "Backup and Reset" in Settings crashes whenever I click on it. Also, I cannot download files from dropbox. After going through 'chown'-ing all the files in /data/media and running 'fix_permissions' script, I was able to get some other apps working.

However, I have no idea how to fix dropbox and the "Backup and Reset" function. Also, there could be potentially more apps somewhat broken.

Is there any other way to reset the rom while leaving all userdata untouched? I am reluctant to wipe my userdata as it takes a lot of time to restore and the restore process seems to cause some permission issues as well. It would be nice if there is some system tool to scan the file system and fix everything rather than only fixing apps defined in 'packages.xml'

Thanks in advance!

Stacktrace for backup manager:

I/BackupManagerService( 307): New app com.android.providers.settings never backed up; scheduling

D/BackupManagerService( 307): Now staging backup of com.android.providers.settings

E/BackupManagerService( 307): Can't write com.android.providers.settings to backup journal

E/BackupManagerService( 307): java.io.IOException: open failed: EACCES (Permission denied)

E/BackupManagerService( 307):	at java.io.File.createNewFile(File.java:940)

E/BackupManagerService( 307):	at java.io.File.createTempFile(File.java:1005)

E/BackupManagerService( 307):	at com.android.server.BackupManagerService.writeToJournalLocked(BackupManagerService.java:4833)

E/BackupManagerService( 307):	at com.android.server.BackupManagerService.dataChangedImpl(BackupManagerService.java:4790)

E/BackupManagerService( 307):	at com.android.server.BackupManagerService.dataChangedImpl(BackupManagerService.java:4763)

E/BackupManagerService( 307):	at com.android.server.BackupManagerService.addPackageParticipantsLockedInner(BackupManagerService.java:1438)

E/BackupManagerService( 307):	at com.android.server.BackupManagerService.addPackageParticipantsLocked(BackupManagerService.java:1413)

E/BackupManagerService( 307):	at com.android.server.BackupManagerService.<init>(BackupManagerService.java:805)

E/BackupManagerService( 307):	at com.android.server.ServerThread.run(SystemServer.java:583)

E/BackupManagerService( 307): Caused by: libcore.io.ErrnoException: open failed: EACCES (Permission denied)

E/BackupManagerService( 307):	at libcore.io.Posix.open(Native Method)

E/BackupManagerService( 307):	at libcore.io.BlockGuardOs.open(BlockGuardOs.java:110)

E/BackupManagerService( 307):	at java.io.File.createNewFile(File.java:933)

E/BackupManagerService( 307):	... 8 more

Error message for dropbox:

E/dbxyzptlk.h.b( 1822): Outputting exception to log: ERROR

E/dbxyzptlk.h.b( 1822): java.lang.Throwable: Failed to delete /data/data/com.dropbox.android/files/anl/gzdbup-1342252425551.dbu

E/dbxyzptlk.h.b( 1822):	at com.dropbox.android.util.h.f(panda.py:1070)

E/dbxyzptlk.h.b( 1822):	at com.dropbox.android.util.h.ax(panda.py:1134)

E/dbxyzptlk.h.b( 1822):	at com.dropbox.android.util.h.ah(panda.py:55)

E/dbxyzptlk.h.b( 1822):	at com.dropbox.android.util.l.run(panda.py:654)

E/dbxyzptlk.h.b( 1822):	at java.util.Timer$TimerImpl.run(Timer.java:284)

F/libc ( 2201): Fatal signal 13 (SIGPIPE) at 0x00000899 (code=0), thread 2201 (sh)

Error saving a file:

E/com.dropbox.android.taskqueue.k( 1822): Error in task: /test.docx: FAILURE