Revert "Parser.Dep: remove wrong logic for FStar.Stubs"

Boy was I wrong. But make it right, these go into FStarC.

src/parser/FStarC.Parser.Dep.fst

@@ -1759,8 +1759,24 @@ let print_full (outc : out_channel) (deps:deps) : unit =
         pr "\n\n"
     in
     let keys = deps_keys deps.dep_graph in
+    let no_fstar_stubs_file (s:string) : string =
+      (* If the original filename begins with FStar.Stubs, then remove that,
+      consistent with what extraction will actually do.
+
+      This is VERY IMPORTANT for krml extraction, since we will generate
+      the krml file even if we're not extracting these files (they are stubs!)
+      per se. Make sure to run karamel tests (or a check-world) if you change this. *)
+      let s1 = "FStar.Stubs." in
+      let s2 = "FStarC." in
+      let l1 = String.length s1 in
+      if String.length s >= l1 && String.substring s 0 l1 = s1 then
+        s2 ^ String.substring s l1 (String.length s - l1)
+      else
+        s
+    in
     let output_file ext fst_file =
         let basename = Option.get (check_and_strip_suffix (BU.basename fst_file)) in
+        let basename = no_fstar_stubs_file basename in
         let ml_base_name = replace_chars basename '.' "_" in
         Find.prepend_output_dir (ml_base_name ^ ext)
     in