Topological order not computed correctly when multiple dfy files present in the command-line

[MikaelMayer]

Dafny version

latest-nightly

Code to produce this issue

// File1.dfy

replaceable module X {
  method getMessage() returns (s: string)
}

module XGo replaces module X {
  method getMessage() returns (s: string) {
    s := "I'm in XGo";
  }
}

// File2.dfy
module Y {
  import X;
  method Test() {
    var message := X.getMessage();
    print message;
  }
}

method Main() {
  Y.Test();
}

Command to run and resulting output

> dafny build -t:lib File2.dfy File1.dfy --output File21.doo

Makes a .doo file containing a program in which module XGo appears after module Y. If you run it in Go:

> dafny run -t:go File21.doo

produces an error in the go files saying module XGo not found because doo files are assumed to be in topological order.

> dafny build -t:lib File1.dfy File2.dfy --output File12.doo
> dafny run -t:go File21.doo

works as expected.

What happened?

The module order when emitting doo files is not topologically sorted when multiple files are provided, it's the order of the provided files.
Historically, this is why some systems are not able to build the .doo files locally, because the find order of the external modules is different. @atomb reported a find order of:

./Concurrent-go.dfy
./Concurrent-notarget-java-cs-js-go-py.dfy
./FileIOInternalExterns-notarget-java-cs-js-go-py.dfy
./FileIOInternalExterns-go.dfy
./FileIO-notarget-java-cs-js-go-py.dfy
`` 

whereas my find order returned:

./Concurrent-go.dfy
./Concurrent-notarget-java-cs-js-go-py.dfy
./FileIO-notarget-java-cs-js-go-py.dfy
./FileIOInternalExterns-go.dfy
./FileIOInternalExterns-notarget-java-cs-js-go-py.dfy

which caused the generated doo files to not work with the CI, but moreover go projects cannot compile with my generated doo files (I'm on Windows using git bash).

### What type of operating system are you experiencing the problem on?

Windows