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
