>
> When you amend the second commit replaces the results of the first. It's
> for the occasion when you commit too early and possibly forget to add some
> files, or you mess up your commit message.


I don't think you're answering on the same level of abstraction as Thiago's
question. At a high level, the commit has indeed been "replaced", but the
commits D and E are both separate entities as far as Git is concerned, it's
just that E's parent has been set to C and D isn't reachable from any ref;
D is in a dangling state.

Try this:

cd /tmp
git init foo
cd foo
touch foo
git add foo
git commit -a -m "Initial commit"
touch bar
git add bar
git commit -a -m "Bar"
git log --oneline

# output:
2e1c949 Bar
499724c Initial commit

git commit --amend
# amend the message to be "Bar (edited)"

git log --oneline

# output:
94e441b Bar (edited)
499724c Initial commit

Now look at the log starting from the commit that was amended (2e1c949):

git log --oneline 2e1c949

# output:
2e1c949 Bar
499724c Initial commit

2e1c949 still exists and still has its parent set to 499724c, it's just
that 2e1c949 is not reachable from, in this case, master. You can see this
more explicitly in the log when specifying master and the dangling 2e1c949:

$ git log --graph --oneline --decorate master 2e1c949 # two explicit places
to start from
* 94e441b (HEAD, master) Bar (edited)
| * 2e1c949 Bar
|/
* 499724c Initial commit

The two are separate, as you can see.

As far as an actual answer concerning `prune` and `fsck`, I'm not quite
sure but it may be something to do with the default length of time before
an object will actually be pruned. I'd be interested in reading a fuller
answer by someone who knows.

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