Prefer `git init` and `git add -A .` to `git init .` and `git add -A`

Bring `git init` invocations in line with examples from the Git
documentation, and future-proof `git add` for Git v2.0.  More details
in the commit messages.  I'm also concerned about:

    $ git push -u nickname master

vs.

    $ git push nicname master

The former is explained as “Push changes from a local repository to a
remote (if `master` doesn't yet exist\ in the remote)”, but that's not
what the `-u` option actually does (it actually sets the upstream
branch, see `git push --help` for details).  I only use `-u` myself
when I'm setting up a branch for a hub pull-request [1,2].  I don't
think the distinction will be important to novice users.

[1]: https://github.com/github/hub#contributing
[2]: https://github.com/github/hub/blob/master/lib/hub/commands.rb#L179