Documentation update: Fixes issue #1557

- Moves entire documentation to Markdown format. Much simpler.
- Fully supports Doxygen 1.8.7+
- All documentation targets updated: user_doc, share/man, doc and doc/refman.pdf.
- Tested across Ubuntu, CentOS and Mac OS.

Output preview:
- [User HTML Docs](http://thebespokepixel.com/fish/user_doc/html/index.html)
- [Man pages (as .zip file)](http://thebespokepixel.com/fish/man1.zip)
- [Developer docs](http://thebespokepixel.com/fish/doc/html/index.html)
- [Developer PDF manual](http://thebespokepixel.com/fish/doc/refman.pdf)
This should probably be `cd user_doc/html && rm -f ...`, no? That way if the `user_doc` folder fails to be created in the first place, this won't attempt to delete files in the current directory.