Scripts running under the CLI version of colony have a process.env object but it is empty. It should probably be filled with a copy of the parent process's whole list.
Current workaround is to put process.env.FOO = "42" lines atop scripts, but this makes sharing code difficult when it comes to private stuff like TM_API_KEY and whatnot.
xref: tessel/t1-cli#167 will tuck specifically-configured variables atop any script that you push/run to a Tessel device.