Allow core specs from command line in atom repository regardless of its location

Previously, when running `apm test` inside the package directory worked fine because it set the `spec-directory` argument to the executable and just ran the core specs. However, if the repository was located somewhere other than `~/github/atom` and no `ATOM_DEV_RESOURCE_PATH` environment variable was defined, it would *first* load a bunch of core files out of the application bundle. Now that we're using custom elements, these leads to errors due to redundant element definition, so we need a new approach.

Now when you run `apm test` in the atom repository, we will automatically assign the resource path to the directory containing the specs unless one is otherwise specified.

Closes #3872

/cc @kevinsawicki since you are the lord of startup. :snowflake::boot: 
Mind keeping the existing sort order of these options?