The index must be in a fully merged state.

Conceptually, git-write-tree sync()s the current index contents into a set of tree files. In order to have that match what is actually in your directory right now, you need to have done a git-update-index phase before you did the git-write-tree.

--missing-ok

Normally git-write-tree ensures that the objects referenced by the directory exist in the object database. This option disables this check.

--prefix=<prefix>/

Writes a tree object that represents a subdirectory <prefix>. This can be used to write the tree object for a subproject that is in the named subdirectory.