I can phrase this in two ways and I'll start with the short way:

Why does a merge of a git submodule use as merge-base the commit that was active in the merge-base of the parent repo, rather than the merge-base of the two commits that are being merged?

The long question is:

A submodule change can be merged, but only if the merge is a "fast-forward" which I think is a fair demand, but currently it checks if it's a fast-forward from a commit that might not be very interesting anymore.

If two branches A and B split at a point when they used submodule commit S1 (based on S), and both then switched to S2 (also based on S) and B then switched to S21, then it's today not possible to merge B into A, despite S21 being a descendant of S2 and you get a conflict and this warning:

warning: Failed to merge submodule S (commits don't follow merge-base)

(attempt at ASCII gfx:

Submodule tree:

S ---- S1
   \ - S2 -- S21

Main tree:

A' (uses S1) --- A (uses S2)
   \ --- B' (uses S2) -- B (uses S21)

I would like it to end up as:

A' (uses S1) --- A (uses S2) ------------ A+ (uses S21)
  \                                     /
   \ --- B' (uses S2) -- B (uses S21)- /

And that should be legal since S21 is a descendant of S2.

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