> Lack of knowledge of why we should get the IOExceptions in the first place ;) 

Then it seems wiser to ignore all sources that fail with a ``IOException``, and keep indexing the next source. We could handle this directly in  [SourceIndexer.indexProject](https://github.com/scala-ide/scala-search/pull/22/files#L12R40). The result of the indexation should still be a ``Failure`` with a custom exception that carries a reference to the sources that couldn't be indexed. It's then up to the caller code to decide what to do with it (for instance, at the moment, we could simply log the name of the files that weren't indexed because of an IOException, so that when it happens we will have some more understanding of what can cause the exception to occur ;)).

Also, we should have a mechanism to inform the user when these sort of error happens. Please, file a ticket about this.