CodePipeline with Github not uploading dot files

I have a Elastick Beanstalk with Linux 2023 ec2 instance and NodeJS 18 app with deployment by CodePipeline and Github 2 so when I commit to staging branch, is auto deployed.

The thing is that I need to set the response timeout higher and everytime I commit, it resets.

So I tried doing .ebextensions/timeout.conf just like this:

files:
  "/etc/nginx/conf.d/elasticbeanstalk/timeout.conf":
    mode: "000644"
    owner: root
    group: root
    content: |
      proxy_connect_timeout 7200s;
      proxy_send_timeout 7200s;
      proxy_read_timeout 7200s;
      send_timeout 7200s;

container_commands:
  01_reload_nginx:
    command: "nginx -s reload"

It is been uploaded to github repo, but when I go to /var/app/current which is the location of the app, .ebextentions is not there (so I guess is kinda a clue) and also there's not a file .puppeteer (it doesn't do anything, is just to test that .files/folders are not been uploaded).

Not sure what to do right now. How to setup the server settings **if .ebextensions are not uploaded. **

I'm really a newbie to cloud. Really appreciate your help!