var pkg = require(process.cwd() + '/package.json');
var intrepidjsVersion = pkg.version;

// Dummy index, only shows intrepidjs-cli version
console.log(intrepidjsVersion);

var pkg = require(__dirname + '/package.json');
var intrepidjsVersion = pkg.version;

// Dummy index, only shows intrepidjs-cli version
console.log(intrepidjsVersion);

Use __dirname instead of process.cwd
Use __dirname instead of process.cwd

process.cwd refers to the directory in which file was executed, not the directory in which it lives