Replace CLI plugin command `run` with `compile`

This PR replaces the broken `run` command (https://github.com/travis-ci/travis-ci/issues/2995#issuecomment-65974868) with the new `compile` command.

The old `run` command considered only stages (and executed them by default), but the new command will compile the entire script and prints it out to STDOUT (except secure environment variables and build matrix). The resulting script should be fit to use on a machine that closely mimics the build VM.

See README for usage.