Parser.Dep: respect fstar.include in directory expansion

The all_fstar_files_in_dir function was unconditionally recursing into
all subdirectories when --dep was given a directory argument. This
changes it to use Find.expand_include_d, which only recurses into
subdirectories listed in fstar.include files.

Without fstar.include, only F* files in the immediate directory are
found. With fstar.include, only the listed subdirectories are traversed
(matching the existing behavior of the include path mechanism).

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Author: Lef Ioannidis

src/parser/FStarC.Parser.Dep.fst

@@ -1696,18 +1696,20 @@ let collect_deps_of_decl (deps:deps) (filename:string) (ds:list decl)
  *   to read the parsing data from checked files
  *)
 
-(** Recursively find all F* files in a directory *)
-let rec all_fstar_files_in_dir (dir:string) : ML (list file_name) =
-  let files = safe_readdir_for_include dir in
-  List.collect (fun f ->
-    let full_path = Filepath.join_paths dir f in
-    if Filepath.is_directory full_path then
-      all_fstar_files_in_dir full_path
-    else if List.existsb (fun ext -> Util.ends_with f ext) (all_file_suffixes ()) then
-      [full_path]
-    else
-      []
-  ) files
+(** Find all F* files in a directory, respecting fstar.include for subdirectory traversal.
+    Uses Find.expand_include_d to determine which subdirectories to visit. *)
+let all_fstar_files_in_dir (dir:string) : ML (list file_name) =
+  let dirs = Find.expand_include_d dir in
+  List.collect (fun d ->
+    let files = safe_readdir_for_include d in
+    List.collect (fun f ->
+      let full_path = Filepath.join_paths d f in
+      if not (Filepath.is_directory full_path)
+        && List.existsb (fun ext -> Util.ends_with f ext) (all_file_suffixes ())
+      then [full_path]
+      else []
+    ) files
+  ) dirs
 
 (** Expand any directories in the command line file list to their contained F* files.
     When a module has both .fst and .fsti, only include the .fsti to avoid