I'm failing to understand why. Here is my story.

I have a small project in version control. I also keep the outline in
version control. I think this is good, the outline serves as skeleton
for the project, it evolves together with the project.

I learned to ignore the diffs related to the header of the outline - I
just don't look at them. I think I already saw on this list other
people complaining about it too, I just don't remember the exact
context to add a reference link to another thread.

But the implications go further. I'm using branching often to emulate
bzr shelve / git stash for putting away some unfinished changes when
I'm in the middle of something. When I'm merging later, the outline
file always produces conflicts. The header that stores data about the
expanded nodes is different and I have to merge raw XML manually,
which is not pleasant.

I can think of a couple of reasons why leo itself is not affected by
this. leo uses those reference files (which I personally consider a
hack that tries to rather dodge the vcs implications than mitigate
them). Also, leo development is mostly linear, not branched, so
conflicts don't happen often.

I will be extremely happy if one day that data goes away from the
outline header. I don't see anymore how the persistence of expanded
nodes has a major positive impact. When closing an outline, it is good
to have a "resume entry point" for the next time, but this is achieved
easily by cloning the node in question into the root, so it stays
visible.

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