Recover from class files and Analysis object getting out of sync.

The #958 describes a scenario where partially successful results are
produced in form of class files written to disk. However, if compilation
fails down the road we do not record any new compilation results (products)
in Analysis object. This leads to Analysis object and disk contents to get
out of sync.

One way to solve this problem is to use transactional ClassfileManager that
commits changes to class files on disk only when entire incremental
compilation session is successful. Otherwise, new class files are rolled
back to previous state.

The other way to solve this problem is to record time stamps of class files
in Analysis object. This way, incremental compiler can detect that class
files and Analysis object got out of sync and recover from that by
recompiling corresponding sources.

This commit uses latter solution which enables simpler (non-transactional)
ClassfileManager to handle scenario from #958.

Fixes #958
simplified settings core example (as per `util/collection` `SettingsExample`)