I really do not have time to look into this for now until late
in the evening, but it is not surprising at all that per-path
partial commit is _always_ slower than the whole tree commit.
It simply needs to do _extra_ work, such as (1) re-initializing
a temporary index from the tree, (2) add the named entries to
that temporary index, and (3) add the same named entries to the
real index. After that it writes a tree out of the temporary
index but the cost for that is the same as writing out of the
real index that is done for the normal commit.
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