Updated mirscanModule.py

Patched mirscanModule.py with code provided in source code website to prevent
known problem described in the documentation. Altered name of variable arguments
*as to standard *args, preventing clash with 'as' keyword.

Added a .gitignore file.
Added #! to executables and an example files folder

The examples are available in:
http://bartellab.wi.mit.edu/softwareDocs/MiRscan3/sampleFiles.tar.gz
and provide examples for each of the file formats used in this package.
Executable interface changed to argparse

Introduced argparse to deal with the variables being passed to the executables.
Additional changes include the move of all non-function code to the end of the
file, renaming of variables (outfile to scoreFile) and the usage of 'with
open(..., w) as output' instead of open(..., w) followed by f.close().
Clean up of store_cut.py

Introduced argparse and made a general clean up to store_cut.py. Updated error
messages in all scripts.
Merge branch 'develop'