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What exactly is a "initial checkout"

I am trying to teach JGit [1] to behave like native git regarding some
corner cases during "git checkout". I am reading the "git read-tree"
documentation and I am not sure about the case [2]. Git should behave
differently during a normal checkout than when you are doing a
"initial checkout". I can imagine that the first checkout you do after
you have cloned a repo is a initial checkout but: What exactly defines
a "initial checkout"? It can't be an empty or non-existing index
because native git behaves like in a non-initial-checkout even if the
index is empty (see example below).

Here are some commands explaining my case. Git is facing an empty
index, HEAD and MERGE (the commit you checkout) have the some content
for path 'p'  and still git is neither updating index nor workingtree
file during checkout.

git init
mkdir p
echo initial >p/a
git add p/a
git commit -m initial
touch p2
git add p2
git commit -m followup
git rm -r p p2
echo "important data" >p
git checkout HEAD~ # successful checkout leaving p dirty
cat p # prints "important data", so 'p' is not updated during the checkout
git ls-files -sv  # empty -> index is empty

[1] https://www.eclipse.org/jgit/
[2] https://github.com/git/git/blob/master/Documentation/git-read-tree.txt#L187