Made a template class to use with SCons

The Manuscript class in templates.py can be used with SCons to build the
required tex file using the given journal template.
2 build commands: 1 for ms and 1 for papers

Instead of having a pretty=True flag, separate the builders into 2
methods. This way the same SConstruct can build both versions when
compiling.

Clean rule for .pyc files.
Added sample versions of the built pdfs
updated readme with usage instructions
Fix trailing ) in journal class list
Merge pull request #1 from pinga-lab/scons

Made a template class to use with SCons