tree-wide: Update to new libglnx fd APIs

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