Angular 2 Typescript SystemJS Coverage Scans Only Loaded Files

Project is angular 2 and it is using a systemjs test shim loader to load the files for the test.
I can't include the app files in the karma.conf.js file because it will break the systemjs loader.

When karma coverage scans, it is only using those files that are loaded by the system js loader, and it is not scanning the entire app directory.

Is there a work around to this issue?

Thanks

Start by reproducing the Angular 2 setup with the SystemJS test shim loader and the karma.conf.js configuration described in the issue. Trace why coverage scans only files loaded by SystemJS, then verify that the entire app directory is included without breaking the loader.

Written by the indexing model from the issue text.