Standardize error handling and console output functions

[victorlin]

Several parts of the code were written prior to the availability of top-level exception handling and shared console output functions. These should be updated.

Tasks

• Replace usage of file=sys.stderr + sys.exit (example) with raise AugurError
• Replace AlignmentError with AugurError (unmerged example)
• Make ConflictingArgumentsException extend AugurError (unmerged example)
• Use the same exit code (both 1 and 2 are used)
• Replace usage of print(file=sys.stderr) with print_err
  • Maybe this should be called print_info instead since the message is informational, only the file stream is stderr
  • Maybe create a new function print_warn to standardize prefixing of messages with WARNING:

Links

• Originally proposed as Use top-level exception handler across all subcommands #1076