Output warnings to a file

[tsmbland]

Currently MUSE produces a few types of warnings when issues arise. These have important information that users need to pay attention to, but currently they get buried in the deluge of messages that MUSE prints so are likely to be ignored

I think warning messages should be outputted to a file so they're easier to see, and to keep a permanent record. To be honest it's probably a good idea to have some kind of log file anyway including information like the MUSE version and Python version, so warning messages can be a part of this