Simplify some `conf` and `md` files.

- `.DS_Store` is not required to ignore in `npm` (`npm` synchronized from git repo).
- `.DS_Store`, `.git` and `node_modules` is not required to ignore in `bower` (`bower` synchronized from git repo).
- `https://github.com/mbostock/d3/issues?milestone=&page=1&state=open` -> `https://github.com/mbostock/d3/issues/new`.

`_site` directory (`.gitignore`, `.npmignore`) used?