checkupdate should update submodules on every checkout

...not just pull HEAD, get submodules and never again update them.

Ref. fdroiddata!4845 (comment 171936258)

Now, I can force it in some places (are these the right places? the only ones?)...

--- a/fdroidserver/fdroidserver/common.py 2019-05-19 16:41:12.470163139 +0300
+++ b/fdroidserver/fdroidserver/common.py      2019-05-19 16:30:00.000000000 +0300
@@ -879,6 +879,7 @@
             if p.returncode != 0:
                 self.clone_failed = True
                 raise VCSException("Git clone failed", p.output)
+            p = self.git(['submodule', 'update', '--init', '--force', '--recursive'], cwd=self.local)
             self.checkrepo()
         else:
             self.checkrepo()
@@ -921,6 +922,7 @@
             raise VCSException(_("Git checkout of '%s' failed") % rev, p.output)
         # Get rid of any uncontrolled files left behind
         p = FDroidPopen(['git', 'clean', '-dffx'], cwd=self.local, output=False)
+        p = self.git(['submodule', 'update', '--init', '--force', '--recursive'], cwd=self.local)
         if p.returncode != 0:
             raise VCSException(_("Git clean failed"), p.output)

...and looks fixed (well at least for Jami)

Thoughts @Bubu @eighthave @uniqx