Attempt to shut down any PC that just threw.

Alleviates the symptoms of error sin the class of #1002016.
Reinstating the JDT reconcile override in ScalaSourceFile.

It's still called by the JDT Indexer. Fixes #1002016.
This is a partial revert of ee2f5a7. See also [this comment](https://github.com/dragos/scala-ide/commit/ee2f5a7606647b0380fad1820d74b29ff01a096c#commitcomment-4675824).
Merge pull request #622 from huitseeker/issue/1002016

Reinstate call to JDT reconciler for side-effects