A rebase regression in Git 2.18.0

Hi,

I’ve found something that may be a regression in git rebase implementation in 2.18.0. First I spotted it on macOS but I can also confirm it happening on Linux. Git 2.19.0.rc0.48.gb9dfa238d is affected too.

In order to trigger it, a repo layout similar to the following is required:

files/
	file1
	file2
	file3
	file4
	file5
project

Let’s call this state baseline. Then, in a branch, let’s edit project file and move file3 to nested/files subdirectory, here’s the final layout:

files/
	file1
	file2
	file4
	file5
nested/
	files/
		file3
project

Let’s get back to master and also edit project file to cause a conflict. After that trying to rebase the branch upon master will cause the following git status output:

rebase in progress; onto baf8d2a
You are currently rebasing branch 'branch' on 'baf8d2a'.
  (fix conflicts and then run "git rebase --continue")
  (use "git rebase --skip" to skip this patch)
  (use "git rebase --abort" to check out the original branch)

Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

	renamed:    files/file1 -> nested/files/file1
	renamed:    files/file2 -> nested/files/file2
	renamed:    files/file3 -> nested/files/file3
	renamed:    files/file4 -> nested/files/file4
	renamed:    files/file5 -> nested/files/file5

Unmerged paths:
  (use "git reset HEAD <file>..." to unstage)
  (use "git add <file>..." to mark resolution)

	both modified:   project

All renames except file3 are invalid and shouldn’t be here. Here’s how the output looks like produced by an older Git version (git version 2.15.1):

rebase in progress; onto baf8d2a
You are currently rebasing branch 'branch' on 'baf8d2a'.
  (fix conflicts and then run "git rebase --continue")
  (use "git rebase --skip" to skip this patch)
  (use "git rebase --abort" to check out the original branch)

Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

	renamed:    files/file3 -> nested/files/file3

Unmerged paths:
  (use "git reset HEAD <file>..." to unstage)
  (use "git add <file>..." to mark resolution)

	both modified:   project

Here’s a ready-to-use repository: https://github.com/nikolaykasyanov/git-rebase-bug.

Regards, Nikolay Kasyanov