Refactor packages

I did a refactoring of the packages because the project was getting pretty large. The new package structure looks like this:

```
+ core
+ debug
+ factors
+ query
    + engine
+ server
+ skyd
    + config
```

This will be especially important in `multinode` since we're adding a bunch of commands. Also, I need to add a parser and some additional AST structs for `query`.

There's now a `Makefile` so you can run `make fmt` and `make test` to format or run all the packages.

[Fixes #107]

/cc: @boourns @orenmazor