I created this report from the git bugreport template following https://git-scm.com/community. Thanks to anyone who takes the time to read and look into this! Please let me know if there are any follow up questions or if anything is unclear. This is my first bug report to git so please let me know if I should have written anything different! What did you do before the bug happened? (Steps to reproduce your issue) I found this when using git subtree to vendor this library (https://github.com/htfy96/dollar), I believe this will also happen in any similar cases where the subtree has a file with an identical path as one of the files in your repo. I was able to repro this from a brand new repository as follows: ```sh mkdir ./test_repo cd ./test_repo touch .clang-format echo 'Any text in this file should work' > .clang-format git commit -m "create .clang-format in main repo" git checkout -b feat_branch git subtree add --prefix dollar_subtree git@xxxxxxxxxx:htfy96/dollar.git master --squash git checkout master touch foo.txt git commit -m "commit anything so that we have something to rebase onto" git checkout feat_branch git rebase master ``` You should see that there is a conflict that needs resolution between the main .clang-format file we created, and the subprojects .clang-format even though the files are in seperate dirs. What did you expect to happen? (Expected behavior) I did not expect a conflict since the .clang-format file we created didn't change. What happened instead? (Actual behavior) There was a conflict between the two files in seperate dirs. What's different between what you expected and what actually happened? The rebase conflict that occured. Anything else you want to add: I think this is happening due to the way git subtree is squash merging in the subproject, even though a git blame on the .clang-format we created doesn't show any changes, it appears that the history conflicts since the path relative to the root is the same in the subproject. Please review the rest of the bug report below. You can delete any lines you don't wish to share. [System Info] git version: git version 2.55.0 cpu: x86_64 built from commit: e9019fcafe0040228b8631c30f97ae1adb61bcdc sizeof-long: 8 sizeof-size_t: 8 shell-path: /bin/sh rust: enabled feature: fsmonitor--daemon gettext: enabled libcurl: 8.21.0 OpenSSL: OpenSSL 3.6.3 9 Jun 2026 zlib-ng: 2.3.3 SHA-1: SHA1_DC SHA-256: SHA256_BLK default-ref-format: files default-hash: sha1 uname: Linux 7.1.8-arch1-3 #1 SMP PREEMPT_DYNAMIC 2026年8月11日 09:16:08 +0000 x86_64 compiler info: gnuc: 16.1 libc info: glibc: 2.44 $SHELL (typically, interactive shell): /usr/bin/fish [Enabled Hooks]