Thanks. That means to me that your project isn't properly configured for source roots. All source files must be found under configured source roots. You can configure your source roots a few different ways:
https://www.jetbrains.com/help/idea/content-roots.html
https://www.jetbrains.com/help/webstorm/configuring-project-structure.html
Please make sure these are properly configured and I bet this issue (and likely others) goes away. Let me know if it doesn't.
IC will warn you if there are no source roots, but if you start adding source to another directory, you must mark it as a source root for IC to know to handle it properly. This becomes even more critical with the more flexible directory structure of SFDX.
I'll see if I can provide better feedback in IC when files are requested for deployment which aren't under a source root as well, but in the interim just make sure that your content roots and source roots are configured properly for your project structure.
Regards,
Scott