Nothing special needs ot be done to run Documon, aside from ensuring that Node is installed on your system.
Download it, unzip it, then run it:
cd "path/to/documon"
node ./index.js "path/to/source/files"
To incorporate Documon into your project / build system use:
cd "/your/project/path"
npm install documon
… this allows you to build documentation from within your project using:
var docs = require("documon");
docs("/path/to/src");