routes.js
module.exports = function(app, passport) {
.......
};

// route middleware to ensure user is logged in
function isLoggedIn(req, res, next) {
    if (req.isAuthenticated()){
        return next();
    }
    else{
      alert("not authernticated");
    }
    res.redirect('/');
}

server.js

var express  = require('express');
var app      = express();
var port     = process.env.PORT || 8080;
var mongoose = require('mongoose');
var passport = require('passport');
var flash    = require('connect-flash');
.......
require('./config/passport')(passport); // pass passport for configuration
.....
// required for passport
app.use(session({
    secret: 'ilovescotchscotchyscotchscotch', // session secret
    resave: true,
    saveUninitialized: true
}));
app.use(passport.initialize());
app.use(passport.session()); // persistent login sessions
app.use(flash()); // use connect-flash for flash messages stored in session

// routes ======================================================================
require('./app/routes.js')(app, passport); // load our routes and pass in our app and fully configured passport