kitctl should resync S3 config before generating

There are cases when someone might loose existing config files on filesyste, running the bootstrap command should first sync these files from S3 to filesystem

Start at the kitctl bootstrap command entry point and trace how configuration is generated and synchronized with S3. The work is done when bootstrap resynchronizes existing configuration files from S3 to the filesystem before generating configuration.

Written by the indexing model from the issue text.