Interface to Zeo++ and GULP, and addition of defects subpackage in analysis

Shyue,
I addressed the issues related to previous pull request. 
a) The tests are working.
b) Defects package is moved inside analysis.
 
I updated comments and tests for io.zeoio, command_line.gulp_caller and analysis.defects.point_defects
modules. defects.point_defects is still a work in progress. Some duplicate functionality is present. Unit tests are missing for some classes. Those classes are not used at present and may be deleted or reworked based on future use.