Update about homebrew.

directory. If neccessary, this can be symlinked to other folders as
well.
- Cleanup in index.rst to make sure whole document build as whole one.
- Cleanup toplevel index.rst. Removed non-existing entries.
- Section numbers is currently disabled. It can be enabled in top-level
`index.rst` file by putting `:numbered:` in ::toc.

directory. If neccessary, this can be symlinked to other folders as
well.
Cleanup in index.rst to make sure whole document build as whole one.

Removed `libsbml-dev` requirement. Also `moosegui` is now `moose`.

Doxygen_1.8.9 is added which should be used to generate doxygen files,Rdesigneur folder is creater under "user" folder and corrected index.rst file is updated, deleted "html" folder,Rdesigneur markdown file with correct date,"snippet " and "tutorial"folder is created with relevant files to generate html files

clean up, all markdown files will be placed under docs/user/markdown, images under /docs/images one can use markdown2rst.py to convert Rdesigner,MooseGui and Kkit docs which places the file under docs/user/GUI and docs/user/Rdesigneur and further one can use makefile to convert to rst to html which will be placed under _build folder in respective folders

added notification about `libxml2-dev`

Fixed grammar and typo.