Changes related to the use of gendered or binary language in the code.

The changes are all related to the use of gendered or binary language in
the comments, messages, and documents (e.g. referring to the user explicitly
as "he" or "he/she").  I searched for thse instances and changed them to
the gender-neutral singular they (http://en.wikipedia.org/wiki/Singular_they).
In the process I fixed quite a few typos that would show up in the
auto-generated documentation.

By Jean-François Caron jfcaron@phas.ubc.ca).