Add `--in-place` flag for in-place re-rendering

To make it easier to maintain different behavious WRT copying and over-writing files, add a flag for this common case. For in-place re-rendering, all we need is a path to a meta.yaml and a target directory. Then, we need to disable copying util/ and allow for over-writing all of README.md, {updata,init}.sh.

(This should be done before #71 (closed).)