$ ls -A

$ git init
Initialized empty Git repository in /home/add/reproattempt/.git/

$ echo -e 'one\ntwo\nthree' | tee alpha | tee beta
one
two
three

$ git add alpha beta

$ git commit -m 'Initial commit'
[master (root-commit) e3f1056] Initial commit
 2 files changed, 6 insertions(+), 0 deletions(-)
 create mode 100644 alpha
 create mode 100644 beta

$ git branch branch

$ git branch
  branch
* master

$ git rm alpha
rm 'alpha'

$ git commit -m 'Deleted alpha'
[master 5592048] Deleted alpha
 1 files changed, 0 insertions(+), 3 deletions(-)
 delete mode 100644 alpha

$ git checkout branch
Switched to branch 'branch'

$ sed -i '/two/d' alpha

$ cat alpha
one
three

$ git commit -m 'Edit alpha' -- alpha
[branch cda6327] Edit alpha
 1 files changed, 0 insertions(+), 1 deletions(-)

$ git merge master
CONFLICT (modify/delete): alpha deleted in master and modified in HEAD. Version HEAD of alpha left in tree.
Automatic merge failed; fix conflicts and then commit the result.

$ git status
# On branch branch
# Unmerged paths:
#   (use "git add/rm <file>..." as appropriate to mark resolution)
#
#       deleted by them:    alpha
#
no changes added to commit (use "git add" and/or "git commit -a")

$ git delete alpha
git: 'delete' is not a git command. See 'git --help'.

$ git rm alpha
alpha: needs merge
rm 'alpha'

$ git status
# On branch branch
# Changes to be committed:
#
#       deleted:    alpha
#

$ git commit  #Deleted the bits from the editor, but I just used the default message
[branch 0fba33b] Merge branch 'master' into branch

$ git branch branch2

$ git log --graph --decorate --all
*   commit 0fba33bbc2e995de7159cedcd04e86869f27c6cd (HEAD, branch2, branch)
|\  Merge: cda6327 5592048
| | Author: me_and
| | Date:   Thu Aug 16 11:16:24 2012 +0100
| |
| |     Merge branch 'master' into branch
| |
| |     Conflicts:
| |             alpha
| |
| * commit 5592048e7089cba2c2a88e05bf0b82a8de7e82e6 (master)
| | Author: me_and
| | Date:   Thu Aug 16 11:13:25 2012 +0100
| |
| |     Deleted alpha
| |
* | commit cda632752e266026a66f8f8433597e83e1d80e2b
|/  Author: me_and
|   Date:   Thu Aug 16 11:13:57 2012 +0100
|
|       Edit alpha
|
* commit e3f10566160bc81587833ea1e026f3e16f4d151a
  Author: me_and
  Date:   Thu Aug 16 11:12:55 2012 +0100

      Initial commit

$ git branch
* branch
  branch2
  master

$ git rebase master
First, rewinding head to replay your work on top of it...
Applying: Edit alpha
Using index info to reconstruct a base tree...
Falling back to patching base and 3-way merge...
Auto-merging beta

$ # Wait, what!? We're merging *beta*? That didn't change!

$ ls
beta

$ cat beta
one
three

$ git checkout branch2
Switched to branch 'branch2'

$ git rebase -i master  # Use the default message. That is "pick cda6327 Edit alpha"

error: could not apply cda6327... Edit alpha

When you have resolved this problem run "git rebase --continue".
If you would prefer to skip this patch, instead run "git rebase --skip".
To check out the original branch and stop rebasing run "git rebase --abort".
Could not apply cda6327... Edit alpha

$ # Now that's more like what I'd expect!

$ git status
# Not currently on any branch.
# Unmerged paths:
#   (use "git reset HEAD <file>..." to unstage)
#   (use "git add/rm <file>..." as appropriate to mark resolution)
#
#       deleted by us:      alpha
#
no changes added to commit (use "git add" and/or "git commit -a")

$ git rm alpha
alpha: needs merge
rm 'alpha'

$ git rebase --continue
Successfully rebased and updated refs/heads/branch2.

$ ls
beta

$ cat beta
one
two
three