How to remove selected commit log entries from a Git repository while keeping their changes?

Question

git-rebase(1) does exactly that.

$ git rebase -i HEAD~5

git awsome-ness [git rebase --interactive] contains an example.

1. Don't use git-rebase on public (remote) commits.
2. Make sure your working directory is clean (commit or stash your current changes).
3. Run the above command. It launches your $EDITOR.
4. Replace pick before C and D by squash. It will meld C and D into B. If you want to delete a commit then just delete its line.

If you are lost, type:

$ git rebase --abort  

# detach head and move to D commit
git checkout <SHA1-for-D>

# move HEAD to A, but leave the index and working tree as for D
git reset --soft <SHA1-for-A>

# Redo the D commit re-using the commit message, but now on top of A
git commit -C <SHA1-for-D>

# Re-apply everything from the old D onwards onto this new place 
git rebase --onto HEAD <SHA1-for-D> master

Here is a way to remove a specific commit id knowing only the commit id you would like to remove.

git rebase --onto commit-id^ commit-id

Note that this actually removes the change that was introduced by the commit.

To expand on J.F. Sebastian's answer:

You can use git-rebase to easily make all kinds of changes to your commit history.

After running git rebase --interactive you get the following in your $EDITOR:

pick 366eca1 This has a huge file
pick d975b30 delete foo
pick 121802a delete bar
# Rebase 57d0b28..121802a onto 57d0b28
#
# Commands:
#  p, pick = use commit
#  r, reword = use commit, but edit the commit message
#  e, edit = use commit, but stop for amending
#  s, squash = use commit, but meld into previous commit

You can move lines to change the order of commits and delete lines to remove that commit. Or you can add a command to combine (squash) two commits into a single commit (previous commit is the above commit), edit commits (what was changed), or reword commit messages.

I think pick just means that you want to leave that commit alone.

(Example is from here)

You can non-interactively remove B and C in your example with:

git rebase --onto HEAD~5 HEAD~3 HEAD

or symbolically,

git rebase --onto A C HEAD

Note that the changes in B and C will not be in D; they will be gone.