This method will end up calling ``removeOccurrencesFromFile`` for all sources in the project. I can't say from where I stand if this could degrade performances, but I think it would be better to delete the whole index for the passed ``proj`` before starting the indexing phase. 

Also, if ``proj`` was already indexed, if an error occurrs while re-indexing it then the index could be in an inconsistent state (for instance it could contain occurrences of the source that just failed to index). Not sure if this issue can actually materialize itself. WDYT?