Refactor Charon database syncing and CharonSession object methods

@vezzi The pilot run is on the sequencer now, so it should be available to play around with this week.

@mariogiov They can use any ([A-Za-z0-9-_]) characters they want at the moment. I thought that underscores were forbidden, but it turns out they are not. I asked Johanna about this now, and they will disallow the underscores in the future, so hopefully this will not be to much of a problem for the IGN projects.

This is the regexp that I've been using on our samples `^(\w+)_(\w+(?:-\w+)?)_L(\d+)_R(\d)_(\d+)\.fastq\.gz$` I'm not to sure how correct it is though. And as you know, the project name is not included in file name.