This commit removes the duplication that happened at the options and options.execOptions level. Now all exec related information lives in options.execOptions.
I've updated all the references and tests that referred to things like options.script, etc.
This also fixes the (new) bug with exec argments not being placed in the right position when the script is detected via a package (so it reads `node --debug app.js` - this is resolved in command.js (due to the flattening of the config).
I've also fixed a few tests that said they were passing, but actually should have failed (but didn't because I was mocking too much of the code).
