doc/use/configuration.rst: multiple changes

* remove references to editing the config file by hand
* update `config list supybot` from Limnoria
* mention `config setdefault` instead of nesting `config default`
* update config search op
* comment `Editing the Configuration Values by Hand`
configuration: add warning about editing registry

and uncomment the section.
Merge pull request #12 from Mkaysi/configuration

doc/use/configuration.rst: multiple changes