This new version of Axonator has an updated command line interface that lets you encrypt entire directories of .trio files!
To use, just specify directories where you would normally specify individual Axon files:
fan afAxonatorExt
-axonIn lib-axonIn/
-axonOut lib-axonOut/
-passPhrase "Axonator Protects"
-keyFunc "(fnName) => return \"gm8v8MePNgSRhVRZ-2zogw\""
Thanks go to Group 14 Engineering for the suggestion.
Have fun!
Steve.