Wordpress permalinks structure changes on git pull

[adenta]

Hi! I am using this script to automate WordPress deploys. For some reason, the permalink structure is being changed on every pull from the server. I am using this git ignore file, which is in the root directory of my project. When I run the deploy script from a browser it appears that more files than I would expect are being pulled, and the gitignore is not being seen.

Hope I am not wasting anyone's time, please let me know if this issue has been seen before, or if this is more of a WordPress question than a deployment questions.

[Croydon]

.gitignore only ignore these files for pushing, not pulling.