Does that only apply to adding new files? The changes in commit A could affect the behavior of the changes in commit B even if they are different files.
No, it applies to everything. If adding patches A and B (same or different files) will lead to same result regardless of which order they are applied, they are called "commutative" and pijul won't care which order they are in your history.
It only tracks content of files, not semantic or behavior changes.
