Use custom help flags in completion scripts

[natecook1000]

This uses the customized help flags when generating completion scripts and includes the --version flag when appropriate. (Fish completions didn't include the help flags at all, which is now fixed as well.)

Checklist

• I've added at least one test that validates that my change is working, if appropriate
• I've followed the code style of the rest of the project
• I've read the Contribution Guidelines
• I've updated the documentation if necessary

[natecook1000]

@swift-ci Please test