The background behind this is around beginning of February 2006, the thread "Two ideas" by Carl Worth. And the current behaviour is defined by this commit. I'll talk about a possible improvement but first, here is what it does: commit 130fcca63fe8e7e087e7419907e018cbbaf434a3 Author: Junio C Hamano <junkio@xxxxxxx> Date: Sun Feb 5 00:07:44 2006 -0800 ... - "git commit paths..." acquires a new semantics. This is an incompatible change that needs user training, which I am still a bit reluctant to swallow, but enough people seem to have complained that it is confusing to them. It 1. refuses to run if $GIT_DIR/MERGE_HEAD exists, and reminds trained git users that the traditional semantics now needs -i flag. 2. refuses to run if named paths... are different in HEAD and the index (ditto about reminding). Added paths are OK. 3. reads HEAD commit into a temporary index file. 4. updates named paths... from the working tree in this temporary index. 5. does the same updates of the paths... from the working tree to the real index. 6. makes a commit using the temporary index that has the current HEAD as the parent, and updates the HEAD with this new commit. ... The check that prevents you from doing $ edit A B $ git update-index A B $ git commit -o B is the rule #2, which I think could use further improvement. It is to address the "committing skewed files" issue Carl brought up in that thread. It might be better to further check if the working tree file is the same as the index, and to allow a commit in such a case. The intent of rule #2 is to prevent this from happening: $ edit A B $ git update-index A B $ edit B again $ git commit -o B When this happens, the real index will have _old_ contents of B that never was committed, and does not match what is in the index. But after the commit, we will match the real index to what was committed, so we will _lose_ the index entry for B before the second edit you explicitly told git to remember by saying 'update-index'. On the other hand, in your original sequence: $ edit A B $ git update-index A B $ git commit -o B B being committed would be different between HEAD and index, but that is what we are going to commit anyway, so after this commit, B will be in sync with the updated HEAD. To put it in another way, "commit -o" is a short-hand for people who do not want to run update-index themselves (IOW, people who just want to use git without worrying about the index file). If you use update-index to mark "this is what I want to commit" yourself, you should do so consistently. If you are not ready to commit A but you want to commit B, do not mark both of them and expect "commit -o" to do magic fixups. - : send the line "unsubscribe git" in the body of a message to majordomo@xxxxxxxxxxxxxxx More majordomo info at http://vger.kernel.org/majordomo-info.html