Updates the type annotation for the `DefaultConfig` type to specify the
allowed values of org_log_done for the Lua LSP. The values that are
specified are based on the currently documented values for `org_log_done`.

Adds a method to the `TodoConfig` type to make determining whether to
log a time, note, or not log at all for a give TodoConfig easier.

Remove the LOGGING property logic from the sections and the file-level.