Prefer RunE over Run for Cobra commands

[jnschaeffer]

Is your feature request related to a problem? Please describe.
Cobra Command structs can use either the Run or RunE fields to run actual commands. Using RunE for commands rather than Run allows us to return errors when commands fail, which can be nicer to work with than using logger.Fatal.

Describe the solution you'd like
All commands that are populated with Run set are populated with RunE set instead.

Describe alternatives you've considered
We can leave things as they are, but it makes commands harder to read and test.