There is no good way to do this. You can create a new project. Then copy in the app/ directory. You won't be able to edit those files inside Architect but you'll be able to make reference to them. e.g. Ext.create('travel.store.StoreCreatedOutsideArch');
I don't know why anyone would ever need to drop to a command line to generate an app/workspace/whatever when using Sencha Architect. I've always just created a new project, enabled the build tools, then it initialises Cmd, and when I click the Build button, it builds a minified project for me. At least that's how it worked in 3.0.4
Now that I've tried 3.1 with Ext 5, repeating this process does not result in a built app, it just nags me constantly for a publish path and never accepts anything I give it. The index.html file created by 3.1 just includes a bootstrap.js file, with no app.js, so its way of building has obviously been modified extensively. Perhaps it's still a work in progress? Or maybe we must now (or always have had to) use "sencha generate ..." and I've just been lucky until 3.1?
This morning the gods have smiled upon me and a fresh Ext JS 5 blank project builds OK. I don't recall doing anything differently. I still have a support ticket open in relation to frameworks in SA 3.1, so I'll wait on that.