Merge pull request progit#592 from JonnyJD/jgit-javadoc

fix jgit javadoc link

Merge pull request progit#89 from schacon/appendix-final

Appendix Final

Merge remote-tracking branch 'origin/master' into appendix

Conflicts:
	book/10-git-internals/sections/refs.asc

Merge pull request progit#43 from schacon/chapter-3-polish

Chapter 3 polish

add atlas.json and cover image