I keep important settings like the hostnames and ports of development and production servers in my version control system. But I know that it\'s bad practice to kee
Provide a way to override the config
This is the best way to manage a set of sane defaults for the config you checkin without requiring the config be complete, or contain things like hostnames and credentials. There are a few ways to override default configs.
Environment variables (as others have already mentioned) are one way of doing it.
The best way is to look for an external config file that overrides the default config values. This allows you to manage the external configs via a configuration management system like Chef, Puppet or Cfengine. Configuration management is the standard answer for the management of configs separate from the codebase so you don't have to do a release to update the config on a single host or a group of hosts.
FYI: Encrypting creds is not always a best practice, especially in a place with limited resources. It may be the case that encrypting creds will gain you no additional risk mitigation and simply add an unnecessary layer of complexity. Make sure you do the proper analysis before making a decision.