Logstash mixing up two configuration files?!

Oh wow, I wasn't aware of that! so you mean it takes all the files and make a huge pipeline out of them?
Okay, that's probably it. I used to have logstash on Windows a year ago, then left it and now I created a logstash server on linux. I remembered that I needed to configure pipline yaml but it just worked, so I never go to do it. this is probably the answer!