edawson/gfakluge: Minor bug fixes and paper edits post-review

This contains some minor changes from the review process:

• [X] make examples.md a link to that file
• [X] set the GitHub website link to the appropriate documentation (now links to README / GitHub Pages)
• [X] make interface.md a link to that file
• [X] bash-tap/bash-tap-bootstrap be included in the source code (made bash-tap) a git submodule, meaning it's now downloaded with git clone --recursive
• [X] You may want to consider using Autotools (I'm going to run through some tutorials and see if I can incorporate this - thanks for the suggestion!)
• [X] make install installs pliib.hpp and tinyfa.hpp
• [X] bump version to 1.1.1
• [X] fix make install instructions