Add: mild handout re-arrange +getting git

Re-ordered some sections in the handouts (ex. help commands at the
start) and changed very very minor formatting in the TeX version.
Added information on getting Git to both handouts. Also added link
to the book.
Fix: formatting on indents +missing newlines

Added indentation on commands for command line that are embedded
in bullets. Also added missing newlines to the section on git log.