Allow non-user packages to be kept in the use data list

By default, we clean up the data from the package-dex-use.list at
every boot. The clean up will remove any obsolete or uninstalled
packages.

Since system server will not show up as a regular app, we need
to add a mechanism to ensure that its dex files are not cleaned up.

Test: atest DexManagerTests PackageManagerTests
Bug: 148774920
Change-Id: I0788163b066af5713b8763f1875338add2d49aa9