Added mkdocs documentation.
Altered doxygen generation (doxyfile and shell script) to work with mkdocs.
Removed the whole html folder thing for docs, now the files reside in the root gh-pages branch.
New readme.
modified merge script to include middlewares, all are included by default
include excludes everything else (items separated by ',')
exclude only excludes selected items (items separated by ',')
using with instead of open and close
removed while loop
using one line to write the new file
using unordered map instead of ordered map
added indentation to the generated file
