Update only PKM source code affected by JML generation
JmlGen overwrites all files it processes: unchanged files are updated, and this is not necessary.
What seems to be a minor optimization can in fact have huge side effects: when updating source code, the PKM deletes all related information in other collections (like commentsjava).
Limiting the number of updates would prevent information loss: moreover, when JmlGen is run twice, there would be no side effect the 2nd time (as the JML generation does not affect a file when JML is already there).