CLI/config: default to storing all config in external files

Previously the fact that some configuration options were only stored
in the database (and thus editing the config file had no effect) was a
source of user confusion. This was fixed with the series ending at
d9af0af1646.

On the other hand, the underlying partition of config options into
those stored by default in the database and those stored in the config
file remained. This is also confusing, since now some invocations of
"notmuch config set" modify the config file, and others silently
modify the database instead.

With this commit, it is up to the user to decide which configuration
to modify. A new "--database" option is provided for notmuch config to
enable modifying the configuration information in the database;
otherwise the default is to update an external config file.