Fix performance issue from refreshing runtime permission state before write.

- The writeRuntimePermissionsForUserLPr() call in
  installPackageFromSystemLIF() doesn't seem necessary at all.
- Call writeLegacyPermissionStateTEMP() only once for all users in
  writePermissionSettings().

Fixes: 172297495
Test: presubmit
Change-Id: I459bc853cd4f72b70fad84bae9fb189dd974cfbf