Webstorm 2016.1 'Generated source files should not be edited'

Since updating to Webstorm 2016.1 some files have this warning when I make changes:

Generated source files should not be edited. The changes will be lost when the sources are regenerated.

So far the affected files are only index.js as shown in this screenshot:

These files are not generated, I have rebuild the project and they don't change.

I did not have this warning in Webstorm 11.

How does Webstorm determine that a file is "Generated"?

Can I disable this feature?

Thanks!