Fix some oversights from #895.

- Always write the configure cache file as it is needed for updating
  the makefile when --update is called.
- List the modules which have been enabled in the "configuration
  complete" message.
- Silence some harmless warnings about installing PEM files which
  don't exist.
Merge pull request #953 from SaberUK/master+configure-oversights

Fix some oversights from #895.