Added short hidden section at beginning of cookbook snippet sections explaining how to run the snippets

* Recovered quickstart section in html, added tutorials placeholder and implemented rudimentary integration between doxygen and sphinx (dependecy on breathe sphinx extension)

* removed recursion limit change

* Added section to quickstart, and fixed a few minor typos in the install page

* Updated installation documentation with new mac osx brew install procedure. Made new section for OSX for consistency of format.

* removed some breathe related stuff from conf.py

* fixed minor typo in wildcard.py

* Recovered rdesigneur tutorial. Modified file by adding extended contents, commented out incomplete sections. Modified rdesigneur snippets page title to 'more rdesigneur examples' instead of just 'Rdesigneur'

* Added autorun statement to Compartment_net.py.

removed pyrun1.py documentation as it is exactly the same as pyrun.py.

updated vec information in quickstart to reflect actual ouput.

* uploaded fixed compartment_net.py without all my comments

* ...

* changed files in docs folder for final version of documentation

* changed the README.txt file.

* changed the path to moose-examples in conf.py and formatting in chem_GUI

* removed docs/source/user/py/introduction/index.rst, and /install/index.rst due to redundency