Improve documentation and investigate behavior of `dope.sh`

[sodic]

There are several strange and undocumented behaviors with dope.sh. Some are desirable, others likely aren't.

1. We've designed dope.sh to ignore package-lock.json in the template directory. This was done on purpose because package-lock.json is only useful for us and we don't ship it as a part of the template.
2. It ignores untracked files. I am not sure if this in on purpose or an accidental side effect. In any case, we should document it in the README.
3. Problems emerge when you rename a file that's in the diff. Doing so creates conflicts that dope.sh doesn't know how to resolve. We should investigate this and fix it or document it.