>Think of each branch as a pointer. Then realize that you can make that pointer point anywhere on the DAG, even to parts of the DAG that have no connection to each other. The `reflog` is a (local, non-comprehensive) history of where that pointer has pointed.
I got that branches were pointers. Now that I'm aware that the DAG is fully represented inside objects, I can see that what's inside logs/ is actually just logs. Each log corresponds to a subgraph of the full DAG. Getting history from a log would be more efficient than from the objects themselves, because to get it from objects, you'd have to dereference a lot of object references.
>I'm not sure what branches living under .git/refs has to do with excessive hierarchies/trees. There are enough things stored in the .git directory, that if you mashed them all together it wouldn't make any sense.
Having to descend through layers of subdirectories makes things harder. I'd reduce the depth of the directory tree to the absolute minimum. It's hard to tell if this is the minimum without knowing exactly what all the implementation constraints might have been.
I can see that the real meat of this system is the object store. It's useful to know about `git cat-file` for inspecting it.