Update versioning and secrets recommendations

[toolmantim]

This updates the readme with the following:

• Move away from beta/stable/edge to 2/3/edge — so people pin to the buildkite agent version they want, and ease the upgrade path for people.
• Adds more environment hook examples, based on people's feedback
• Updates the security recommendations, nudging people not to use environment variables and command line flags
• Includes a git-credentials file example in addition to an SSH key example
• Mentions the tini caveat that entrypoint files can't have file extensions

[thewoolleyman]

It would be easier to review this if you squashed all the commits down to one:

• git fetch
• git rebase -i origin/master
• "fixup" all the commits except the top-most one into the top-most one.

Then I could easily just look at the single commit here, without having to compare this branch to master to see what has changed.