> Are you in cygwin or the windows "shell"?

cygwin shell. With windows "shell" Cmd.exe the output differs but it fails
as well:

[KC:\ocamlmgw\bin\menhir: unknown option `-modules mlutils/globParser.mly'.
Usage: C:\ocamlmgw\bin\menhir <options> <filenames>
...[CUT]...
$B"+(J[KExit code 2 while executing this command:
  C:/ocamlmgw/bin/menhir --raw-depend --ocamldep "ocamldep -modules" mlutils/glo
bParser.mly > mlutils/globParser.mly.depends

In ocamlbuild/my_std.ml there is a comment about the problem:

let sys_command =
  match Sys.os_type with
  | "Win32" -> fun cmd ->
      let cmd = "bash -c "^Filename.quote cmd in
      (* FIXME fix Filename.quote for windows *)
      let cmd = String.subst "\"&\"\"&\"" "&&" cmd in
      Sys.command cmd
  | _ -> Sys.command

We could use Unix.create_process. I attached a function
to split cmd in a list. 

Regards,
Christoph Bauer

let split_quoted_string_list ?(quote = '"') s =
  let len = String.length s in
  let word_buffer = Buffer.create 128 in
  let rec outer i acc =
    if i >= len then List.rev acc
    else
      let c = String.unsafe_get s i in
        match c with
            ' ' | '\t' | '\r' | '\n' -> outer (i+1) acc
          | c when c = quote -> inner (i+1) acc
          | _ -> plain i acc
  and end_of_word i acc =
    let word = Buffer.contents word_buffer in
      Buffer.clear word_buffer;
      outer i (word::acc)
  and inner i acc =
    if i >= len then failwith ("parser error (split_quoted_string_list): " ^ s);
    let c = String.unsafe_get s i in
      if c = quote then end_of_word (i+1) acc
      else
        (Buffer.add_char word_buffer c;
         inner (i+1) acc);
  and  plain i acc =
    if i >= len then end_of_word i acc
    else
      match String.unsafe_get s i with
          ' ' | '\t' | '\r' | '\n' -> end_of_word (i+1) acc
        | c when c = quote -> end_of_word i acc
        | c -> Buffer.add_char word_buffer c;
            plain (i+1) acc
  in outer 0 []