There's another PR that makes the changes needed for the Phar file:

https://github.com/wp-cli/wp-cli/pull/619/files#diff-b5d0ee8c97c7abd7e3fa29b9a27d1780L15

https://github.com/wp-cli/wp-cli/pull/619/files#diff-986376432265e5dc6280fc5d8f50566eR40