Conduit: Duplicate logger output

[winder]

When starting Conduit with no arguments, there are duplicate error outputs:

{"__type":"Conduit","_name":"main","level":"info","msg":"Data Directory:  ","time":"2022-09-16T15:50:51-04:00"}
Error: supplied data directory was empty
ERRO[0000] supplied data directory was empty

Some initial investigation:

The first line is us trying to log the config after we've loaded it: https://github.com/algorand/indexer/blob/conduit/cmd/conduit/main.go#L69

The Error message is the validity function finding the data directory in the config empty: https://github.com/algorand/indexer/blob/conduit/conduit/config.go#L27

And the third line is probably from https://github.com/algorand/indexer/blob/conduit/cmd/conduit/main.go#L122
Seems like we've got a bunch of duplicate logs of the same thing I guess? Since we are using a logger initialized in the init function we should probably always be using that.

We are also using RunE instead of Run in conduit, which is probably where one of the error outputs comes from. But it is not clear to me why the format is different.