Use .streamline.json when running too

Not just registering. Fixes #195.

This means both running files and running the REPL. And I have to say, this finally feels *amazing*.

Before:

```
$ time _coffee example/
real	0m9.887s
user	0m9.043s
sys	0m0.304s
```

After:

```
$ time _coffee example/
real	0m1.091s
user	0m0.992s
sys	0m0.110s
```

(`example/` is some code of ours, not this repo's `examples` directory.)

I especially love the speedup in the REPL! Because the whole point of the REPL is quick experimentation. =)

PTAL @bjouhier. Lemme know if you'd like the implementation to be any different. Thanks!
I changed the `registerOnly` flag from a formal option to a parameter just for the two internal functions that use it.

Honestly, the main reason was just naming: now that command.js is calling `register()` instead of `run()`, but it wants to run too, it felt weird to say `register()` with `registerOnly: false`. What else would `register()` do? =)

So now it calls `register()` passing `runAlso` as `true`, while that calls `run()` passing `registerOnly` as `false`.

I think there's definitely room for refactoring / cleaning up this logic of `register.register` and `underscored.run` (the bulk of the registration actually happens in `underscored`, and `register` is pretty light), but I didn't want to make too heavy changes in this PR.