Some plugins insert dependencies not on the file system about express-middleware-rollup HOT 3 CLOSED

This sounds indeed like a serious issue. I will investigate whether these pseudo-paths are explicitly part of the rollup system

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I think your idea involving filter is a little too superficial in general. The most robust solution would be to test all the dependencies we got from the rollup bundle if they actually exist - but only AFTER a successful compilation, because failing bundle compilations might be due to a non-existing file. This is how we can make sure that we only consider real file dependencies. One problem with this is that we would always rebuild the bundle on the first load when the dependency cache is still empty (because there hasn't been a successful build yet). We can add a heuristic here to improve this, though, similar to what you have suggested: .filter(id => isValidFileName(id)), where isValidFileName can be arbitrarily complex.
All these considerations aside: The current implementation of allFilesOlder definitely needs to be more robust. We never check if a file exists, only its modification time.

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Agreed. isValidFileName(id) looks reasonable. We could elaborate it in the future, if needed.

I've found path.isAbsolute() is also useful for this purpose.

const isValidFileName = id => path.isAbsolute(id);
const dependencies = bundle.modules
  .map(module => module.id)
  .filter(id => isValidFileName(id));

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