fix: stage deleted files with libgit2

[mvanhorn]

Update the existing stage_file primitive to distinguish a path that still exists in the repository worktree from a tracked path that has been removed. Continue using the current index add operation for present files, but remove an absent tracked path from the index before performing the existing index write so the deletion becomes staged. When a reviewed, tracked file has been removed from the working tree, :stage reaches the libgit2 staging adapter and fails because that adapter unconditionally asks the index to add the missing path. The Git CLI backend already handles this case through git add -- <path>, so the defect is specific to the default libgit2 backend.

A tracked and committed file is deleted from the worktree, then staged through the libgit2 primitive: the call succeeds and the file is absent from the index relative to HEAD, representing a staged deletion; An existing new or modified file is staged: the current add-to-index behavior continues to succeed and the path remains present in the index.

Fixes #638

AI was used for assistance.

[agavra]

Thank you @mvanhorn for the contribution! This looks good to me.