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-impl-system-generator.c

@@ -164,7 +164,7 @@ _ostree_impl_system_generator (const char *ostree_cmdline,
   /* Prepare to write to the output unit dir; we use the "normal" dir
    * that overrides /usr, but not /etc.
    */
-  glnx_fd_close int normal_dir_dfd = -1;
+  glnx_autofd int normal_dir_dfd = -1;
   if (!glnx_opendirat (AT_FDCWD, normal_dir, TRUE, &normal_dir_dfd, error))
     return FALSE;