`diff-hl-flydiff-mode` with `diff-hl-amend-mode` shifts highlights three lines up

[saolaolsson]

When enabling diff-hl-mode (20260328.1925, minimal config, git) and setting diff-hl-reference-revision to "HEAD^" (or using diff-hl-amend-mode):

diff-hl-flydiff-mode disabled: Correct highlights are shown.
diff-hl-flydiff-mode enabled: Correct highlights are shown but all are shifted three lines up.

[dgutov]

Hi! I haven't been able to reproduce this yet.

Could you show some example with a file and a couple of diffs? Or a test repo. But I could take the file, apply the diff, commit, apply the second one and see how the highlights differ with/without diff-hl-flydiff-mode.

[dgutov]

Perhaps include your Emacs version as well.

[saolaolsson]

I've tested it on 29.3 (official Ubuntu 24) and 30.1 (self-built) on one system and the problem is still present. I've now also tested it on 30.1 on a current Debian on a DIFFERENT system and the problem is NOT present there, but I don't see why this is so.

Do you have a suggestion on how I can debug this further? What would cause the highlighted lines to be shifted?

[dgutov]

Perhaps the difference is in the contents of the files? Or in the line endings different between the two repositories on the systems with 30.1? Are you testing with the same file with the same changes in it? You could try comparing the outputs of M-x diff between them, paying attention to the numbers in the hunk headers as well.

…

On Fri, Apr 24, 2026, at 2:44 PM, Ola Olsson wrote: *saolaolsson* left a comment (dgutov/diff-hl#274) <#274 (comment)> I've tested it on 29.3 (official Ubuntu 24) and 30.1 (self-built) on one system and the problem is still present. I've now also tested it on 30.1 on a current Debian on a DIFFERENT system and the problem is NOT present there, but I don't see why this is so. Do you have a suggestion on how I can debug this further? What would cause the highlighted lines to be shifted? — Reply to this email directly, view it on GitHub <#274 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACCMBLNGP434EWPG2Q73G34XNOTHAVCNFSM6AAAAACX5GTPPCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DGMJTGIZTINZRHE>. Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS <https://github.com/notifications/mobile/ios/AACCMBP3W2ZVNVWPMBZ62DT4XNOTHA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTIMZRGMZDGNBXGE42M4TFMFZW63VHMNXW23LFNZ2KKZLWMVXHJKTGN5XXIZLSL5UW64Y> and Android <https://github.com/notifications/mobile/android/AACCMBN52ETW7HTARZ53QAL4XNOTHA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTIMZRGMZDGNBXGE42M4TFMFZW63VHMNXW23LFNZ2KKZLWMVXHJLTGN5XXIZLSL5QW4ZDSN5UWI>. Download it today! You are receiving this because you commented.Message ID: ***@***.***>

[saolaolsson]

I seem to have been confused by old versions of diff-hl. The three-line offset is introduced in this commit, with a minimal config, on Emacs 30.1. Prior to this, the alignment is correct.

[dgutov]

Perhaps you can make a screencast, to show your files and operations? If the config is indeed minimal.

I still cannot reproduce it.

[saolaolsson]

The following snippet will reproduce the problem I am seeing. There seems to be a timing element to it that I didn't notice previously as the highlights will look okay immediately upon opening the file, but editing the file (usually a single edit will suffice) will cause the HEAD~1 diff (but not the HEAD diff) to shift three lines up.

The latest master branch commit will also reproduce the issue but gives additional warning messages (missing functions) on startup. Tested on self built "GNU Emacs 30.2.50 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.41, cairo version 1.18.0) of 2026-06-04".

mkdir diff-hl-issue-274
cd diff-hl-issue-274
git init
printf >file.txt "1\n2\n3\n4\n5\n6\n7\n8\n9\n10\n" && git add file.txt && git commit --message "First commit"
printf >file.txt "1\n2\n3\n4\n55\n6\n7\n8\n9\n10\n" && git add file.txt && git commit --message "Second commit"
printf >file.txt "1\n2\n3\n4\n55\n6\n7\n8\n9\n10\n11\n"
cat <<EOF >init.el
(modify-all-frames-parameters '((background-mode . dark)))
(use-package diff-hl :ensure t :demand t
:vc (:url "https://github.com/dgutov/diff-hl" :rev "cab7b665f979d8ed683a59e56d997ad8b663fa5e")
:config (global-diff-hl-mode) (diff-hl-flydiff-mode) (diff-hl-set-reference-rev "HEAD~1"))
EOF
emacs --init-directory . file.txt

[dgutov]

@saolaolsson Thanks for the attempt, but I still can't reproduce. Doing "a single edit" keeps the reference highlight on the same line:

Tested with Emacs 29, 30 and a development snapshot.

Now, to be frank I now remember seeing a problem vaguely like that maybe a month or two ago, but not in the recent couple of weeks. So please double-check if the issue is still there. If so, we can investigate deeper - e.g. logging the produced diffs to a file, seeing what could be wrong at that stage.

Just as a point of reference, my Git is 2.43.0. Is yours newer or older?

[saolaolsson]

Often two or three edits of the buffer (not file) is required. That alone suggests a timing issue to me.

I see the problem on master also (checked again today).

git version is 2.43.0, with no configuration changes.

[dgutov]

All right. When that happens again, could you copy and post the corresponding contents of buffers *diff-hl-diff* and *diff-hl-reference*? Both names start with a space.

[dgutov]

You could also open them in nearby windows while editing and see how their contents change.