This guide assumes you still have the default files created by on the ExMachina first launch, as follow:

scripts/
├── commands
│   ├── runplayer.js
│   └── runscript.js
├── globals
│   ├── exmachina.js
│   └── some_global_script.js
├── example
│   ├── greetings.js
│   ├── some_other_script.js
│   └── some_script.js
└── utils
    └── bukkit.js

Creating a script is as simple as dropping the JS file inside the scripts/ folder located in <server>/plugins/ExMachina. You can then reference this script using its path relatively to the scripts/ folder without extension.

scripts/
├── example
│   ├── **brand_new_script.js**
│   ├── greetings.js
│   ├── some_other_script.js
│   └── some_script.js

Run this script using the command /exmachina runscript example/brand_new_script in game, from a command block from the server console.