Relates to #135
Low priority, it's probably not a blocker for anyone since workarounds are possible.
First, for using tools like Flow the import paths in the source code need to correspond to actual paths pointing to the correct files. The mapping in manifest.json and the (in the examples heavy) use of "plain imports" of the style import ... from "Module", where the location of "Module" is described in the manifest file, does not work with other source code level tools.
Second, when I have a nested directory structure with relative path imports down the hierarchy, and other imports (possibly to the same files!) within a lower level directory, then I cannot easily tell manifest.json what ./ means since it is different on every level.
Q: Is this even feasible given your implementation choices?