I have never used cloud9, but I think you can just use terminal to install phalcon. Follow the directions described here under "Ubuntu":
https://phalcon.io/en/download
For me it worked without and problems in demo projects:
1) Add PPA in terminal
2) Update sources and install
sudo apt-get update
sudo apt-get install php5-phalcon
3) Validate
[email protected]:~/workspace (master) $ php -i | grep phalcon
/etc/php5/cli/conf.d/20-phalcon.ini,
phalcon
phalcon.db.escape_identifiers => On => On
phalcon.orm.column_renaming => On => On
phalcon.orm.enable_literals => On => On
phalcon.orm.events => On => On
phalcon.orm.exception_on_failed_save => Off => Off
phalcon.orm.not_null_validations => On => On
phalcon.orm.virtual_foreign_keys => On => On
phalcon.register_psr3_classes => Off => Off
I hope that's what you are looking for.