I am also having this problem. Only it has progressively gotten worse to the point where the cursor locks up at the start of my project because it is trying to add whitespace to every single file in my extensive project. I had to force quit Cursor.
Version: 2.1.44
VSCode Version: 1.105.1
Commit: f6a8593b2b7c61c2063c79d5a8fcd248c9db4580
Date: 2025-12-01T22:52:09.315Z
Electron: 37.7.0
Chromium: 138.0.7204.251
Node.js: 22.20.0
V8: 13.8.258.32-electron.0
OS: Darwin arm64 25.1.0
Also having this same issue of modifying whitespace in hundreds of files on startup. Itās been a issue for months - starting to become a dealbreaker especially when it results in potentially hours of time spent reviewing ws changes mixed with actual changes - please prioritize this issue!
How has this issue not been fixed yet ? Itās been months.
Hello everyone, some of my colleagues and I are experiencing the same issue and itās very annoying. In every project, new empty lines keep appearing. I even found a file from a Vibe coder with 56 empty lines at the end. WTF.
Today, some of my teammates told me they had to discard changes because of those new lines, which ended up overwriting work from several sessions. What a waste of time and money caused by such a trivial bug.
Cursor IDE
Letās say I had an open session with cursor IDE. During that session, 15 files were modified. I did not click āKeep Filesā, but simply committed the changes and then continued writing code manually. I close the cursor IDE and re-open it. All of those files that cursor touched will get CR/LF or new line changes applied to them
CR/LF new lines should not be added
Windows 10/11
Version: 2.1.47 (user setup)
VSCode Version: 1.105.1
Commit: 2d3ce3499c15efd55b6b8538ea255eb7ba4266b0
Date: 2025-12-04T02:31:50.567Z
Electron: 37.7.0
Chromium: 138.0.7204.251
Node.js: 22.20.0
V8: 13.8.258.32-electron.0
OS: Windows_NT x64 10.0.26200
No - Cursor works, but with this issue
Glad I am not the only one - this is extremely annoying. It doesnāt keep me from using Cursor, but it sure makes me want to stop using it.
Cursor IDE
When we open a project with open files, Cursor alters them by appending new lines making git think they changed, requiring tedious undo operations to separate them from files with actual changes.
This makes me loathe to ever use the update feature while working.
This is a longstanding issue. Please fix
Have open files
Restart cursor
Files should not be modified
Windows 10/11
Version: 2.1.47 (user setup)
VSCode Version: 1.105.1
Commit: 2d3ce3499c15efd55b6b8538ea255eb7ba4266b0
Date: 2025-12-04T02:31:50.567Z
Electron: 37.7.0
Chromium: 138.0.7204.251
Node.js: 22.20.0
V8: 13.8.258.32-electron.0
OS: Windows_NT x64 10.0.26200
ALL
No - Cursor works, but with this issue
Having the same issue. this is super irritatingā¦
Same here with new lines on startup.
Version: 2.1.48
VSCode Version: 1.105.1
Commit: ce371ffbf5e240ca47f4b5f3f20efed084991120
Date: 2025-12-04T19:26:27.263Z
Electron: 37.7.0
Chromium: 138.0.7204.251
Node.js: 22.20.0
V8: 13.8.258.32-electron.0
OS: Linux x64 6.17.9-300.fc43.x86_64
It seems that those are files that were modified recently. Fixing the files and restarting Cursor modifies the same files again.
Really frustrating, especially with files modified inside submodules that results in submodules looking modified in the umbrella repo.
Also happening to me and I havenāt been able to use the fix that seems to work for some people (Review ā Accept All Changes on all previous agent conversations) because now the āAccept All Changesā option has been replaced by āCommitā.
But I donāt want to commit a couple dozen files with no changes beyond the addition of a newline. 
I was only able to solve this problem by deleting the entire workspace ~/.config/Cursor/User/workspaceStorage and then logging in again.
Of course, almost everything reset, but at least the problem didnāt recur.
I also noticed that I encountered a similar problem when running two background agents simultaneously. Apparently, thereās something still not perfect in this area.
Still happening, I had to nuke the workspace I was using, and was driving myself insane until I found this thread, thought it was a .git corruption issue, git index remote/local conflict or something else. In my case it was only happening to 12 files in the repository, it was always those same 12 files.
I couldnāt find the chat that modified those to try to accept changes or anything, every time I reloaded the window a new line was added to all these files.
Honestly, I hope this is resolved because itās extremely annoying to work like this. Specially in December when we are doing MAJOR refactors and cleanup to our codebase, this becomes extremely cumbersome to deal with.
FWIW - if you go back through all your old agents and keep all the files. It stops happening.
Possibly one of those chats created on an old version of cursor, so might have been fixed with an update? But the behaviour exists still for chats created on that version? No idea.
Just tested with a new agent chat, changed a file, saved (Didnāt keep changes in chat left it un-kept), reopened cursor and it didnāt add a new line.
