diferença entre app.js e index.js no nó.js

tenho uma lógica de negócios a ser executada e configurei as rotas dentro do ficheiro routes/index.js onde pretendo configurar a rota /filter-reports. Por favor, ajuda-me a perceber onde estou a ir mal. Preciso de carregar o ficheiro usando o {[9] } também executar a minha lógica de negócio presente no índice.js arquivo.

App.código-fonte js:

var express = require('express');
var path = require('path');
var favicon = require('static-favicon');
var logger = require('morgan');
var cookieParser = require('cookie-parser');
var bodyParser = require('body-parser');
var _ = require('underscore');
var cache = require('js-cache');
var multer  = require('multer');

var routes = require('./routes/index');
var users = require('./routes/users');

var app = express();

app.all('*', function(req, res, next) {
  res.header("Access-Control-Allow-Origin", "*");
  res.header("Access-Control-Allow-Headers", "X-Requested-With");
  next();
});


// view engine setup
app.set('views', path.join(__dirname, 'views'));
app.set('view engine', 'jade');

app.use(favicon());
app.use(logger('dev'));
app.use(bodyParser.json());
app.use(bodyParser.urlencoded());
app.use(cookieParser());
app.use(express.static(path.join(__dirname, 'public')));

app.use('/', routes);
app.use('/users', users);
var done=false;

app.use(multer({ dest: './uploads/',
rename: function (fieldname, filename) {
  return filename+Date.now();
},
onFileUploadStart: function (file) {
  console.log(file.originalname + ' is starting ...')
},
onFileUploadComplete: function (file) {
  console.log(file.fieldname + ' uploaded to  ' + file.path)
  done=true;
}
}));

// catch 404 and forward to error handler
app.use(function(req, res, next) {
  var err = new Error('Not Found');
  err.status = 404;
  next(err);
});

app.post('filter-reports',function(req,res){
console.log('Working on the filtered reports....');
  if(done==true){
    console.log(req.files);
    res.end("File uploaded.");
  }
});

/// error handlers
// development error handler
// will print stacktrace
if (app.get('env') === 'development') {
  app.use(function(err, req, res, next) {
    res.status(err.status || 500);
    res.render('error', {
        message: err.message,
        error: err
    });
});
}

// production error handler
// no stacktraces leaked to user
app.use(function(err, req, res, next) {
  res.status(err.status || 500);
  res.render('error', {
    message: err.message,
    error: {}
  });
});


module.exports = app;





var express = require('express');
var request = require("request");
var _ = require('underscore');
var jscache = require('js-cache');
var schedule = require('node-schedule');
var filename;

no índice.ficheiro js

var router = express.Router();

router.post('/filter-reports', function(req, res) {
  console.log('Came inside the Node js router.. Now.. its all up to me to format the data....');
    // console.log(req.files);
    //  console.log('Came insode the filter-reports app url >>>>');
    // if(done==true){
    // console.log(req.files);
    // console.log('Files uploaded succesfully ....');
    //res.end("File uploaded.");
    //  }
});

a minha estrutura de pacotes é a seguinte:

app.js  bin  node_modules  package.json  public  routes  views

{
  "name": "nodetest1",
  "version": "0.0.1",
  "private": true,
  "scripts": {
  "start": "node ./bin/www"
 },
  "dependencies": {
  "express": "~4.2.0",
  "static-favicon": "~1.0.0",
  "morgan": "~1.0.0",
  "cookie-parser": "~1.0.1",
  "body-parser": "~1.0.0",
  "debug": "~0.7.4",
  "multer": "~0.1.6",
  "jade": "~1.3.0"
  }
}