• Rollup Version: 1.0.0
• Operating System (or Browser): chrome macOS
• Node Version: 10.8.1

How Do We Reproduce?

I have an issue with rollup even before the last update. I'm making source maps for declaration files and also for esm,cjs, etc files. but for modules, source maps generate empty and invalid files.
something like this:
{ "version": 3, "file": "index.module.js", "sources": [], "sourcesContent": [], "names": [], "mappings": ";;;;;;;;;..........
You can see my project in this repo on develop branch.