Cows-mkgen is able to track dependencies only when file names for functions verbatim (), include (), fsize (), fdate (), exec(), evalexec() are provided as string constants (e.g. foo.html) or via the inputfile () and outputfile () functions.
Otherwise, a warning is raised and you are left with at least four choices:
forget the warning if you're not interested in losing the dependency (this is very dangerous, in my opinion);
provide the file name as a string constant or via the inputfile () and outputfile () functions, if it's possible and reasonable (this is very likely to introduce difficulties in updating since file names will be hard-coded within sources);
decide to update the page every time you run Make (regardless to dependencies) via the __ALWAYS__ directive (see Section 6.6.3);
explicitly tell Cows-mkgen about the dependency via the __DEP__ directive (see Section 6.6.4).
Moreover, if external files introduce further dependencies Cows-mkgen miss them (it can't interpret every scripting language!) so you have to use one of the techniques above.
This manual can be downloaded from http://www.g-cows.org/.