1. Reuseability
Helper.js is a good thing to share code within a bundle - but not across many bundles. I think a strong library concept is still missing. Actually it's not possible to use CDN due to CSP but they are planning to introduce whitelists. It even looks like whitelists could be already possible:
Requesting CSP Exceptions
If your app is not working due to a CSP violation, contact Salesforce
to request a CSP exception for your org. Include the violation message
from your browser's developer console in any communication.
You can use Static Resources to provide libraries (package- or org-wide).
2. Testing
since it's very js-centric you might use some JS testing frameworks - but I expect salesforce to deliver here somthing.
3. Metadata / IDEs
All the Lightning metadata is available via Tooling API:
Alternatively access via Metadata API is working, too.
As far as I know, Force.com IDE still missing Lightning support. I think they are still on v30 or v31
You might also try a plugin for sublime/Mavensmate.
And CodeFusion actually does support Lightning since last year - however by design still without local files ;-)
But you need this package for lightning support - both, metadata and tooling API (v32) is supported.
I always planned to write a version control integration, but probably before that happens I'm going to open source the project.
A really cool thing about Lightning is the speed for saving files. It's not like apex or visualforce which needs about 3 to 10 seconds to save. Try saving a Lightning file it usually takes 0.300 to 0.800 seconds. First time fun coding! Doug's team unleashed a turbo here.
There is a marker interface that your component needs to implement in order to make it available to Lightning App Builder.
<aura:component ... implements="flexipage:availableForAllPageTypes">
I've not done it, but my assumption is that you just add it to your existing implements attribute with a comma.
Best Answer
An App is essentially a specialized top-level component. It comes with the same code structure that a component does, including both a helper and a controller.
These entities can of course be empty if they're not required. However, the app often plays a "coordinating" role amongst its child components, and it may (for example) handle application events. These needs would be supported by the application's controller and helper, which might fire other events, call methods on the public API of its child components, set attribute values, and so forth.
A single Lightning component bundle would include only one helper and one controler.