Add a timeout flag for deployment checks

Currently the timeout is hardcoded for helm deploy and we need to be able to pass that as a flag or through config.yaml file.

Start by locating the hardcoded timeout used by Helm deployment checks and review how command flags and config.yaml are handled. Done means users can provide the deployment-check timeout through a flag or config.yaml and the Helm checks use that value.

Written by the indexing model from the issue text.