Include files are fine; in fact tup automatically handles that for static headers (i.e. header files that aren't generated as part of the build process).

One example of what I'm talking about is what another commentor mentioned: .java files will generate separate .class files for each inner-class in the file, so given "foo.java" you can't tell which .class files will be output when compiling "foo.java" without looking at the contents of "foo.java"

I actually originally had a Makefile with predeps/build/install targets where the "build" step just called tup. People complained that "if tup is supposed to replace make, why are you using make?" I switched it to predeps.sh/build.sh/install.sh and everybody shut up. I personally think it's less ergonomic but don't care enough to argue with a different person every week.