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Don't double check for flags in the manifest
With the recent support for r/w flags in xml files we started checking for flags in the manfiest twice since we already had code specifically handling flags in the manifest. This disables the new code when it is the manifest. Test: Automation Flag: EXEMPT bugfix Bug: 396992602 Change-Id: I55c1358ab38c8f35dd7ede77488feff5ad080d76