Bootstrapping doom with an literate configuration

### What did you expect to happen?

I expected that on a clean install of doom (ie `doom install && doom sync` with a "fresh" `~/.emacs.d/`) the literate config in `$DOOMDIR` would be seen, tangled, and then used -- if not in the `doom install` at least in the `doom sync`.

### What actually happened?

When I ran `doom install` it created new config files (`init.el`, `config.el`, `packages.el`) and used those as my config. Then on running `doom sync` the literate config was ignored.

### Describe your attempts to resolve the issue

I was able to "bootstrap" the literate config by modifying the stock `init.el`. I added `:config literate` and then reran `doom sync` (actually did a `SPC-h-r-r`).

### Steps to reproduce

1. Clean slate (either a new computer with no `~/.emacs.d/` or run `rm -rf ~/.emacs.d`
2. Clone Doom EMacs
3. `doom install`
4. `doom sync`
5. `emacs`
6. Be surprised by your missing configuration.

### System Information

https://pastebin.com/jCnJRwCA