Initialize ServerConfig::EmptyTag using the init list
Add ServerLimits constructor that reads limits from a ConfigTag and use it
Pass the empty tag to Limits when constructing a ServerConfig, remove default ServerLimits constructor
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.
Merge branch 'master+serverlimits'