Fixes majority of PackageManagerTests

Adds QUERY_ALL_PACKAGES to packagemanager tests and fixes some test
logic to match a recent change in the location that apps are installed.

Also added PackageManagerTests to presubmit and suppressed a few
outstanding failing tests that will need to be addressed before closing
the associated bug.

Bug: 152007236
Test: atest PackageManagerTests
Change-Id: I919881810f00a2ff96acd6d44b1794451eb95882