Ports Clean Command to Core

It's all in the title, bro. Ports the clean command to Core and updates the Makefile to get everything to compile as we would like. Addresses #49.
Should change this constant to `cHARNESS_DIR`. Make it an alias for now. i.e. in `cli_constants.ml` do:
```
let cOUTPUT_DIR = ...
let cHARNESS_DIR = cOUTPUT_DIR
```