A while ago, I set up Apps2SD on my ADP, and while I am not sure what, I must have done something wrong, because afterwards, Android refused to boot properly, claiming that the file system permissions of pretty much all installed packages didn’t match up:

Package x.y.z has mismatched uid: 10089 on disk, 10079 in settings

Here’s the Python script I used to apply the file system permissions that Android expected. It iterates over the packages defined in your devices /data/system/packages.xml. Use at your own risk.

"""Parse Android's /data/system/packages.xml file and spits out
shell code to fix UIDs.

This helps you fix "Package x.y.z has mismatched uid: 10089 on disk, 10079
in settings" errors.
"""

from xml.dom import minidom

xmldoc = minidom.parse('packages.xml')

packages = xmldoc.getElementsByTagName('package')
ignored = []
for package in packages:
    try:
        userId = package.attributes['userId'].value
        is_shared = False
    except KeyError:
        userId = package.attributes['sharedUserId'].value
        is_shared = True

    # do not touch permissions of shared apks (they userid always seems to be 1000)
    if not is_shared:
        print "busybox chown %s:%s %s" % (userId, userId, package.attributes['codePath'].value) 

    for subdir in ('', 'databases', 'shared_prefs'):  # note we don't touch lib/
        print "busybox chown %s %s:%s /data/data/%s/%s" % (
            '-R' if subdir else '', userId, userId, package.attributes['name'].value, subdir)