tree-wide: Update to new libglnx fd APIs

This ends up a lot better IMO.  This commit is *mostly* just
`s/glnx_close_fd/glnx_autofd`, but there's also a number of hunks like:

```
-  if (self->sysroot_fd != -1)
-    {
-      (void) close (self->sysroot_fd);
-      self->sysroot_fd = -1;
-    }
+  glnx_close_fd (&self->sysroot_fd);
```

Update submodule: libglnx

Closes: #1259
Approved by: jlebon

src/libostree/ostree-repo-checkout.c

@@ -782,7 +782,7 @@ checkout_tree_at_recurse (OstreeRepo                        *self,
       }
   }
 
-  glnx_fd_close int destination_dfd = -1;
+  glnx_autofd int destination_dfd = -1;
   if (!glnx_opendirat (destination_parent_fd, destination_name, TRUE,
                        &destination_dfd, error))
     return FALSE;
@@ -947,7 +947,7 @@ checkout_tree_at (OstreeRepo                        *self,
        * exists.
        */
       int destination_dfd = destination_parent_fd;
-      glnx_fd_close int destination_dfd_owned = -1;
+      glnx_autofd int destination_dfd_owned = -1;
       if (strcmp (destination_name, ".") != 0)
         {
           if (mkdirat (destination_parent_fd, destination_name, 0700) < 0