Zsh and Prezto files don't always reside in `~/`. Instead, they have
a more spec compliant location (`${ZDOTDIR:-$HOME}/`). Make them
unambiguous in the documentation. Likewise, for `$GNUPGHOME`.
Further, add instruction for optionally setting up Prezto in
`$XDG_CONFIG_HOME`.
While at this, also add clarification on relative ordering of some of
the modules, apply more formatting tweaks and doc improvements.