update.sh: Fix updating logic for checkerframework files.

The previous CL (commit e6b59050 )
had two issues:
 - only jar but not sources.jar files were downloaded
 - new files were added, but old ones were not removed.

This CL fixes both problems.

Test: Checked that "git status" indicates that the same number
      of files are now added as deleted by:
      ./update.sh 2.1.2 9-dev-r4023-3 2.2.2
Bug: 69485063

Change-Id: If045ae03cbf8830eb6468ffc9b73478213df53c9