Updated tutorial and added option to make all tutorials.
Added a function to trim prody package/module names from functions/classes.
Cleaned up configuration file.
Updated ProDy tutorial files.
Updated configuration files.
Updated ignore list.
Normalizing pdb file paths.
Added log message.
Added some doctests.
Fixed a problem with external link configuration.
Updated tutorial make files.
Revised ENM Analysis tutorial.
Copied IPython directive files, changed tempfile use for tracking docs.
Updated Sphinx configurations.