delete-old-files.js

var https = require('https');

// CONFIGURATION #######################################################################################################

var token          = '';
var delay          = 300; // delay between delete operations in millisecond

// GLOBALS #############################################################################################################

var baseApiUrl    = 'https://slack.com/api/';
var fileListApiUrl= baseApiUrl + 'files.list?token=' + token + '&count=1000';
var deleteApiUrl  = baseApiUrl + 'files.delete?token=' + token;
var files         = [];
var thirtyDaysAgoTimeStamp = (new Date().getTime() - (1000 * 60 * 60 * 24 * 30)) / 1000;

// ---------------------------------------------------------------------------------------------------------------------

function deleteFile() {

  if (files.length == 0) {
    return;
  }

  var fileId = files.shift();

  https.get(deleteApiUrl + '&file=' + fileId, function (res) {

    var body = '';

    res.on('data', function (chunk) {
      body += chunk;
    });

    res.on('end', function(){
      var response = JSON.parse(body);

      if (response.ok === true) {
        console.log(fileId + ' deleted!');
      } else if (response.ok === false) {
        files.push(fileId);
      }

      setTimeout(deleteFile, delay);
    });
  }).on('error', function (e) {
    console.log("Got an error: ", e);
  });
}

// ---------------------------------------------------------------------------------------------------------------------

https.get(fileListApiUrl + '&ts_to=' + thirtyDaysAgoTimeStamp, function(res) {
  var body = '';

  res.on('data', function (chunk) {
    body += chunk;
  });

  res.on('end', function() {
    var response = JSON.parse(body);

    for (var i = 0; i < response.files.length; i++) {
      files.push(response.files[i].id);
    }

    deleteFile();
  });
}).on('error', function(e) {
  console.log("got an error: ", e);
});

Thanks for this. I created a fork via https://gist.github.com/dominikwilkowski/76d99ae84848c39e54494f4dbdd4327d

I just developed a bot that helps you to manage this, any contribution is welcome!
https://github.com/danibram/scrapy-slack-bot