Rework error and debug handling

[pjcdawkins]

Choices:

• Do not silence Cobra errors
• Remove stdlib log use
• Make debug logging consistent with legacy CLI format
• Consistently use Cobra command output writers, and make them colorable when possible

Rationale:

• DX issues found when implementing Add a config:install command #226 (this PR is extracted from that, to reduce its size)
• Various issues were caused by silencing errors, like Silent failure when unable to access the temporary directory #177 and Display errors from setting up temporary files in Init() #222
• The color package wants a colorable output writer to be used, but we sometimes need to replace os.Stderr with io.Discard in the root command so that the --quiet option works, so we need output to go through the Cobra cmd writers.