git-pull-after-squash-merge

Fix git pull After Squash Merge

Problem

After a PR is squash-merged to main, switching branches or pulling fails with:

error: The following untracked working tree files would be overwritten by merge:
    data/results/experiment_1.json
    data/results/experiment_2.json
    docs/findings/analysis.html
Please move or remove them before you merge.

These files ARE on main (from the squash merge) but git sees them as untracked locally because squash merge creates a new commit hash — the original branch commits never appear in main's history.

Context / Trigger Conditions

This happens when:

• A branch created new files (not just modified existing ones)
• The branch was squash-merged (not regular merge) to main
• You're on a different local branch that also has those files (from cherry-picks, worktree remnants, or the original branch)
• git pull or git checkout main refuses to proceed

Common scenarios:

• Working on branch B while branch A (which created new files) gets squash-merged
• Checking out main after a parallel session merged files you also have locally
• Multiple Claude Code sessions creating overlapping experiment result files

Solution

⚠️ Safety first — diff CONTENT, not just existence, before removing. An untracked file that exists on main is not necessarily identical to your local copy. A long-stale branch's local copy often has unique edits (a 1-line SHA reference, a draft note). Blindly rm-ing / git clean -fd / reset --hard destroys that content silently. The default instinct (and Options 2-4 below) skip this check — don't.

Option 1: Diff each blocking file against main, back up differers, then remove

# For each blocking file: compare LOCAL untracked copy vs origin/main's version
f=path/to/blocking/file
if git diff --quiet --no-index <(git show origin/main:"$f" 2>/dev/null) "$f" 2>/dev/null; then
  echo "IDENTICAL to origin/main — safe to rm"
  rm -f "$f"
else
  echo "DIFFERS — back up the local copy before removing (it has unique content)"
  mkdir -p /tmp/untracked-backup/"$(dirname "$f")"
  cp "$f" /tmp/untracked-backup/"$f"
  git diff --no-index <(git show origin/main:"$f" 2>/dev/null) "$f"  # eyeball what's unique
  rm -f "$f"   # only after backing up
fi
git checkout main && git pull   # or: git merge --ff-only origin/main