Your mind is designed/evolved to wander, it’s a feature, not a bug, So don't worry too much about that. In meditation, especially for beginners, it’s about how many times you catch yourself and bring your focus back to your anchor. More the merrier, every distraction is just another opportunity to practice.

This is bloody true for myself. One of the main ingredients of unhappiness in my life is this false sense of expectation, because somewhere in my mind I have been told that I'm capable and I should be keep trying!

Did you try Obsidian for personal data management?

The reality is, the organizational structure likely to change over time, then would anyone want to mirror it in the repo structure?

Not likely, no.