Can system apps be enabled/disabled directly from the filesystem?

Whether an app is enabled or disabled is stored in a single file /data/system/users/0/package-restrictions.xml.

I took the following steps to re-enable the Google App and solve my bootloop problem:

1. Boot the Android-x86 virtual machine in debug mode (i.e. append DEBUG=2 to the GRUB entry)




2. mount the filesystem:

   
   
   

   su
   
   
   
   cd /dev
    # these are necessary to "refresh" the environment
   
   cd ..
   
   # otherwise the following commands wouldn't work
   
   
   
   mkdir temp
   
   mount /dev/block/sda1 temp
   
   




3. Edit the package-restrictions.xml file with vi:

   
   
   

   vi /temp/android-6.0-rc1/data/system/users/0/package-restrictions.xml
   
   

   
   
   
   
   

   • Find the entry containing <pkg name="com.google.android.googlequicksearchbox" enabled="3" enabledCaller="com.android.settings">

   
   

   • Move the cursor to the end of that line (Line 13 in my case) and press a to begin editing (see Basic vi commands)

   
   

   • Remove the enabled and enabledCaller attributes. The resulting line should be <pkg name="com.google.android.googlequicksearchbox">

   
   

   • Press Esc and type :wq and press Enter to save and exit vi

   
   



4. Type exit and hit Enter (twice) to boot to Android normally.