CLC-2055 Tweak capistrano deploy script

Capistrano failed strangely on the ./upgrade.sh command, as seen in logs here:

https://bamboo.media.berkeley.edu/bamboo/download/MYB-CLCMVPDEVDEPLOY-DEPLOYCALCENTRALDEV/build_logs/MYB-CLCMVPDEVDEPLOY-DEPLOYCALCENTRALDEV-558.log

This is an attempt to fix.