libfetchers: represent unfetched submodules consistently

Unfetched submodules are included as empty directories in archives, so they end
up as such in the store when fetched in clean mode. Make sure the same happens
in dirty mode too. Fortunately, they are already correctly represented in the
ls-files output, so we just need to make sure to include the empty directory in
our filter.

Fixes: https://github.com/NixOS/nix/issues/6247
Change-Id: I60d06ff360cfa305d081b920838c893c06da801c

src/libfetchers/git.cc

@@ -232,7 +232,7 @@ std::pair<StorePath, Input> fetchFromWorkdir(ref<Store> store, Input & input, co
         if (S_ISDIR(st.st_mode)) {
             auto prefix = file + "/";
             auto i = files.lower_bound(prefix);
-            return i != files.end() && (*i).starts_with(prefix);
+            return (i != files.end() && (*i).starts_with(prefix)) || files.count(file);
         }
 
         return files.count(file);