Not everything from the vault should go to the repository. For instance: your workspace settings should stay private as they change every time you open a new file. Similarly, you 10 Notes/Inbox file - which is similar to a scratch buffer - should stay private as well. Also, currently, the calendar entries that are stored in the 00 Planner/ folder are currently considered private.
If you need to have some specific file ignored, you may decide to add your own entry to .github in a section that starts with a comment, e.g.
# John Doe ignore list
or something similar. Try to be specific and consider placing the content you need to have ignored under the 10 Notes folder temporarily, e.g. 10 Notes/JhonDoe and then ignore that whole folder in .gitignore. It is wise to consider keeping your private stuff in a private vault and keep the Codex vault more suitable for the team content.