You're looking for the two-tree git read-tree -um.  It uses a base tree, (generally you feed it HEAD), a target tree, and (implicitly) the index and worktree.  The table describing its behavior was hard for me to understand so I have my own cheatsheet for it, a reformatted one that makes more sense to me, anyway.  At any rate, it implements git checkout.
git read-tree -um H M  # `I` is the (implicit) index, GIT_INDEX_FILE
                    Legend
        H       Original tree (usually HEAD:)
        I       Indexed tree
        M       Merge target tree
        H->I     \
        H->M      } status in second relative to first
        I->M     /
        "-"     file exists in neither
       new      exists only in second
       deleted  exists only in first
       same     exists in both, unchanged
       changed  exists in both, different
      (blank)   irrelevant or all cases not otherwise given
        keep    keep current version
        fail    whole command fails, no changes
       delete   delete worktree file
      H->I      H->M      I->M
                          same     keep
     deleted   changed             fail
     deleted   deleted             delete
     deleted    same               delete unless Index empty, else use M
                same               keep
      same     changed             worktree clean: use M; dirty: fail
      same     deleted             worktree clean: deleted; dirty: fail
      new        -                 keep
      new       new      changed   fail
     changed   changed   changed   fail
     changed   deleted             fail
note: "index empty" identifies an initial checkout, where HEAD has been
set but never loaded.  git can't currently distinguish between a
delete-everything index and an initial-checkout index.