EDIT (version 2)
It works for me with Sencha Cmd 220.127.116.11 and ExtJS 6.0.1, but only if the js file is in the app folder. In a subfolder, it does not work, __unless__ you add
TL;DR in app.json:
From the documentation:
"path": "someesternalsource.js" // it works
"path": "somesubfolder/someesternalsource.js" // it does NOT work
"includeInBundle": true // it DOES work
When you add extra files, there are some optional properties that indicate how the build process will treat them. For example, in the above case, "library.js" will be included in the concatenated build output and removed from the runtime manifest.
If instead you removed "includeInBundle", then "library.js" would be assumed to reside in your app folder and would then be copied to the build output folder. The entry would remain in the manifest and be loaded separately by the Microloader.