I am trying to incorporate Phundament with an existing database. After some digging around I am able to get it running, but I can't figure out how best to modify the theme - specifically the main menu - in a way that will allow it to be at least somewhat "future proof"...
I could "brute force" (changing ownership etc..) the _menu.php in app/themes/layouts but that seems kinda hack-ish.
No, this is the way it is meant to be.
All theme files are copied on installation into your project, therefore also layouts/_menu.php.
Note: They still exist in /vendor, but they are not used.
Since it's very likely to modify these files heavily, especially the menu, which is even in this basic version rather complicated, it would be nearly impossible to "update" these files later on with a newer version from p3bootstrap.
Note: I am the main developer of Phundament, if you'd like to elaborate more on this topic please create a p3bootstrap issue on github or a posting on phundament-dev.