Due to constant updates from to the Pokemon App the community-driven API-cracking has died off.
Bossland guys have created and are actively maintaining a special service to enable Bots to work with latest API updates.
Only downside is that using the service will cost at least 3.95€/month and every bot user has to buy their own license from them via the following links:

Pay with Paypal or Credit CardAlternative methods (AliPay, Яндекс.Деньги etc)
150 requests/minute 1-month license 150 requests/minute 1-month license
500 requests/minute 1-month license 500 requests/minute 1-month license
1000 requests/minute 1-month license 1000 requests/minute 1-month license
Every time Bot sends data to the pokemon server it does 1 request. Every request needs to be signed correctly to look like the real app.
Regular botting uses up to 30 requests/minute meaning you can use the same license for up to 4 accounts. Gym attacking makes 60 requests/minute.

After you have received the license code, paste it into PokeBot.Ninja and you should be all set to use the newest and safest API.
All the existing donation levels and codes will remain valid and are separate of the Bossland hashing license.