Run dos2unix on *.py and tidyup some files.

[tomgreen66]

Been helping a user run this code on our systems at Cardiff University and hit a few issues:

1. The common issue of ^M newline characters causing problems if you run ./mtag.py rather than python ./mtag.py. Running dos2unix across all .py files fixed a couple of files. This could be fixed using git configuration options to convert newline characters on clone depending on system but opinion online seemed to be divided whether that is a bit cumbersome.
2. The .pyc is not required and added a .gitignore file to stop similar files being added.

Hopefully others will find this useful.