Warn if files with “store” persistence would conflict with files in the worktree

[sellout]

Even though these files won’t actually conflict, having files in both the Nix store and the worktree can lead to confusing and inconsistent behavior.

E.g., if clang-format is configured via Project Manager to look up its configuration in the Nix store, but there is also a .clang-format file in the worktree (whether committed or not), running clang-format outside of a Project Manager environment will use the configuration from the worktree while running it inside a Project Manager environment will use the configuration from the Nix store.

Warnings would alert users to these inconsistencies early. And there should be a configuration option to silence the warning for any or all files that could trigger this.