Debugger code does not handle checked exceptions in many places

I've added a number of FIXMEs notes in the debugger codebase where checked
exceptions are not handled.

Furthermore, I've added a couple of comments that should help better understanding
some of the assumptions we have in the debugger module (this is related to the discussions
that happened in the [PR #219](https://github.com/scala-ide/scala-ide/pull/219))

Re #1001487