Please describe the problem.

This is a repo under git-annex assistant control and was committing and pushing fine but then stopped... there were many other oddities (some files were git rmed and never committed back etc), but now it is at the level of git on remote I guess, so likely going through git-annex filter-process -- claims to have unstaged changes when git status says none:

reprostim@reproiner:/data/reprostim$ git push typhon
Enumerating objects: 15079, done.
Counting objects: 100% (10929/10929), done.
Delta compression using up to 4 threads
Compressing objects: 100% (6763/6763), done.
Writing objects: 100% (6764/6764), 816.02 KiB | 16.00 MiB/s, done.
Total 6764 (delta 64), reused 6388 (delta 1), pack-reused 0
remote: Resolving deltas: 100% (64/64), completed with 30 local objects.
To typhon:/data/repronim/dbic-reproflow/sourcedata/reprostim-reproiner
 ! [remote rejected]     master -> master (Working directory has unstaged changes)
error: failed to push some refs to 'typhon:/data/repronim/dbic-reproflow/sourcedata/reprostim-reproiner'
reprostim@reproiner:/data/reprostim$ ssh typhon git -C /data/repronim/dbic-reproflow/sourcedata/reprostim-reproiner status
On branch master
Your branch is ahead of 'reproiner/master' by 2906 commits.
  (use "git push" to publish your local commits)

nothing to commit, working tree clean

how to troubleshoot in the future?

workaround done: pushed as another branch which I then just "merged" (was fast-forward) locally (on typhon).

What version of git-annex are you using? On what operating system?

reprostim@reproiner:/data/reprostim$ git annex version | head -n 1
git-annex version: 10.20251114-1~ndall+1
reprostim@reproiner:/data/reprostim$ ssh typhon git annex version | head -n 1
git-annex version: 10.20250416