Added example and template files

Added also some __init__.py files. They indicate folder as packages in
PyDev.
Small updates in example files
Small update in example_main_module.py
Reformatted SegmentBySegment.py

Created main() and parse_args() functions. Changed documentation to
docstrings and removed warnings from static analysis. See change history
for version 0.34.
Tested by comparing output files with the previous script. Was the same
except of time stamps and outputpaths.
Removed option twiss from getsuper.py

For details see issue #15
Changed option twiss to twissfile in getsuper test

Since I removed twiss option from getsuper I changed tests/getsuper to
use twissfile instead of twiss.
Removed getsex1200.out in GetLLM

Further small changes in GetLLM and added module docstring.
Added documentation to getsuper.py
Added docstrings to some functions
Merge branch 'master' into alangner