golang.org/x/tools/cmd/stringer doesn't support this. Quoting from its doc:
With no arguments, it processes the package in the current directory. Otherwise, the arguments must name a single directory holding a Go package or a set of Go source files that represent a single Go package.
Easiest solution would be to put all enum values in the same package. You may use separate files, but they must be in the same package.
If you want / must use multiple packages, you can only do this with
stringer if you use different types, each defined in the package in which you list the constants.