fsatrace lint errors shows many missing needs in the rule for various dependencies.mk files. NOTE, this rule runs the ghc .. -M .. dependency generation command. The lint errors are complaining that hs-boot files are accessed while generating dependencies (i.e. while running ghc .. -M ..). These specific lint errors are NOT complaining about ghc .. -M .. forgetting to output hs-boot files, though that may be the case and would be a slightly different issue.

In general this is an annoying problem where the dependencies of dependency generation is often closely related to the output. This is a bit of a chicken and egg problem that I've been meaning to document here in the wiki.