LOTS of code cleanup
- moved some AMBER specific environmental setup into the amberio module
- separated out the parsing of AMBER specific command file specifications into its own function. Will probably need this later.
- added the ability to read AMBER-US style harmonic biases from a file instead of as a string in the command file, as requested by alpha testers
- cleaned up file I/O routines in pj_async_re.py, these really shouldn't be methods, but I've kept dummy methods there so as not to break the existing IMPACT code
- re-tooled _gibbs_re_j so as not to require knowledge of the async_re_job object, this information is now passed as an argument
- re-tooled doExchanges to be more robust to changes in replica status. I'm not sure if this was ever a problem, but since the pool of exchanging replicas is assumed to be static, it is really perilous to keep checking for "self.replicas_waiting_to_exchange", as that attribute is re-computed each time and therefore COULD change in principle. Now a static, local copy of this list is kept.

TODO:
- Break out the replica exchange code into its own module?