Update CLI args of customize

[atanasdinov]

• Adds default value (/config) to --config-dir parameter, allowing for omitting the flag when running Elemental3 from a container
• Adds a short alias -o to --output parameter
• Removes --customize-output parameter for now, as the directory is always cleaned up once the process exits

In the future, we might consider readding --customize-output or something similar if we have to expose any of the intermediate contents.