This moves a lot of machinery for commands into a context.Context with other struct values. This allows for PreRunE's to reliably load the configuration and avoids use of global vars.
This adds experimental file filters which are not guaranteed under our stability policies. These filters take effect after reading the files and before parsing their content.
This fixes an issue where certificate_chain values can't be defined as secrets. While not expressly needed for certificates, it's more convenient and less prone to error than defining a environment variable with the contents.
James Elliott