Move mPermissionTrees to permission settings

Move more state / logic into the permission sub-package. We're
close to being able to wholesale move large amounts of code from
package manager into the permission manager.

Bug: 63539144

Test: Manual. Builds and runs
Test: cts-tradefed run commandAndExit cts-dev -m CtsAppSecurityHostTestCases -t android.appsecurity.cts.PermissionsHostTest
Test: cts-tradefed run commandAndExit cts-dev -m CtsPermissionTestCases
Test: cts-tradefed run commandAndExit cts-dev -m CtsPermission2TestCases
Test: bit FrameworksServicesTests:com.android.server.pm.PackageManagerSettingsTests
Change-Id: Id292441ff22b14665fd77f700ad934bf2c5a3357