Don't crash when one of the configuration files is empty (#7341)

If the admin adds a `.yaml` file that's either empty or doesn't parse into a dict to a config directory (e.g. `conf.d` for debs installs), stuff like https://github.com/matrix-org/synapse/issues/7322 would happen. This PR checks that the file is correctly parsed into a dict, or ignores it with a warning if it parses into any other type (including `None` for empty files).

Fixes https://github.com/matrix-org/synapse/issues/7322