Git rebase

git-rebase

Overview

The standard fixup workflow is: create a fixup! commit in the branch, then GIT_SEQUENCE_EDITOR=true git rebase -i --autosquash <base>. Manually editing the todo file or writing a custom sequence editor script is almost never necessary and introduces failure modes.

Core principle — reconstruct, don't merge. Every pattern below for rearranging commit contents rests on one idea: rather than replaying patches through three-way merge (which conflicts the moment surrounding context has shifted), take each file's complete, correct state — or a clean per-target slice of it — and commit that directly. No merge means no conflicts. When a procedure says "why this works," this is why.

Safety

Before any rebase, note current HEAD:

git log --oneline -1  # copy this SHA

Recovery after a bad rebase:

git reflog              # find the pre-rebase HEAD@{N}
git reset --hard HEAD@{N}

Never rebase while parallel agents have staged changes. Staged changes are shared working-tree state. If another agent commits while you're mid-rebase, the commits become entangled. Finish or abort all rebase operations before handing off to parallel agents.

Before You Start: Audit Per-File Targets

One fixup commit can squash into exactly one target commit. If your working-tree change to a file needs to land in multiple historical commits, you need multiple fixup commits — each containing only the slice that belongs in its target.

This is the single most common cause of mid-rebase conflicts. Catch it upfront:

# For each file you've modified, see which branch commits already touched it
git status --short | awk '{print $2}' | while read f; do
  echo "=== $f ==="
  git log <base>..HEAD --oneline -- "$f"
done

If a file appears in only one commit: a single fixup is fine. If a file appears in N commits: you'll need to split the diff across N fixups. See Splitting One Working-Tree Change Across Multiple Fixup Targets below.

Core Workflow

1. Create the fixup commit

# Stage your changes, then:
git commit -m "fixup! <exact subject of target commit>"

The message after fixup! must match the target commit's subject verbatim. git commit --fixup <sha> generates this automatically.

2. Verify the fixup is in the rebased range

git log <base>..HEAD --oneline | grep "fixup!"

If it's not listed, the autosquash will silently have nothing to squash. See "Dropped fixup recovery" below.

3. Autosquash

GIT_SEQUENCE_EDITOR=true git rebase -i --autosquash <base>

GIT_SEQUENCE_EDITOR=true accepts the autosquash-generated todo without opening an editor. Git arranges the fixup line correctly on its own. No custom script needed.

4. Verify the result

git log --oneline -10          # find the new SHA (rebasing rewrites SHAs)
git show <new-sha> --stat      # confirm expected files are in the right commit

"Rebase succeeded" ≠ "rebase did what I intended." Always inspect the commit.

On long branches with many fixups, prefer incremental autosquash. Commit one fixup, autosquash, verify, then create the next. Batching seven fixups and running one autosquash means conflicts surface in arbitrary mid-rebase order with no cheap way to course-correct — if fixup #1 turns out to span two commits, you discover it three commits into the rebase instead of before starting.

Dropped Fixup Recovery

If a fixup commit was dropped from the branch by a previous rebase:

Don't try to manually insert the old SHA into the todo file. Instead, re-create the commit from scratch:

# Find the dropped commit
git reflog | grep "fixup!"

# Inspect it
git show <dropped-sha>

# Re-apply its changes to the working tree
git checkout <dropped-sha> -- <file>    # for file changes
# or apply the diff manually

# Create a new fixup commit
git add <file>
git commit -m "fixup! <target subject>"

# Now autosquash normally
GIT_SEQUENCE_EDITOR=true git rebase -i --autosquash <base>

Custom GIT_SEQUENCE_EDITOR Scripts

Avoid them. --autosquash handles standard fixup! cases without any script. Custom scripts are only needed when you want non-standard rearrangements.

If you must write one, it must be two-pass:

#!/usr/bin/env python3
import sys, re

todo_path = sys.argv[1]
with open(todo_path) as f:
    lines = f.readlines()

# PASS 1: build map of fixup targets → fixup lines, collect non-fixup lines
non_fixup = []
fixups = {}  # target_subject → [fixup_line, ...]
for line in lines:
    m = re.match(r'^pick (\S+) fixup! (.+)\n', line)
    if m:
        target = m.group(2)
        fixups.setdefault(target, []).append('fixup ' + m.group(1) + ' fixup! ' + target + '\n')
    else:
        non_fixup.append(line)

# PASS 2: insert fixup lines after their targets
result = []
for line in non_fixup:
    result.append(line)
    stripped = line.strip()
    if stripped and not stripped.startswith('#'):
        subject = stripped.split(None, 2)[2] if len(stripped.split(None, 2)) == 3 else ''
        for fixup_line in fixups.pop(subject, []):
            result.append(fixup_line)

# Append any unmatched fixups rather than silently dropping them
for lines_list in fixups.values():
    result.extend(lines_list)

with open(todo_path, 'w') as f:
    f.writelines(result)

The single-pass trap: Processing the todo top-to-bottom fails when the target commit appears before the fixup! line (i.e., always — the target is older). A single-pass script will check if fixup: for the target line when no fixup has been seen yet, store the fixup, and never emit it.

Choosing a Reconstruction Pattern

The next three sections rearrange commit contents. They all apply the "reconstruct, don't merge" principle above; pick by what you start from:

You have…	…and want to	Pattern
A branch mixing formatting and logic changes	A pure reformatting commit first, then code-only commits	Replay-and-reformat
Existing commits whose files belong in different commits	Recombine file states across those commits	Checkout-and-reconstruct (Moving File Changes)
One uncommitted edit	Slice it across multiple historical commits	Per-slice fixups (Splitting)
One edit that is a mechanical, idempotent transform (rename, formatter)	Auto-slice it across the commits it touches	git rebase --exec shortcut

Inserting a Reformatting Commit Before Code Changes

Replay-and-reformat. When a branch mixes formatting changes (e.g., from ruff format, black) with logic changes, split them into a pure reformatting commit followed by code-only commits. Do not cherry-pick or rebase the code commits onto a reformatted base — every hunk conflicts because the surrounding context changed (quotes, line wrapping, indentation), producing dozens of unresolvable conflicts. Reconstruct instead:

# 1. Note current HEAD for safety
git log --oneline -1

# 2. Create a branch at the commit just before code changes
git checkout -b temp-branch <last-pre-code-commit>

# 3. Create the reformatting commit
<formatter> <files>
git add <files>
git commit -m "Reformat with <tool>"

# 4. Replay each code-change commit by checking out its file state
#    from the original branch, reformatting, and committing
for sha in <code-commit-1> <code-commit-2> ...; do
    git checkout "$sha" -- <files>
    <formatter> <files>
    git add <files>
    msg=$(git log -1 --format="%B" "$sha")
    git diff --cached --quiet || git commit -m "$msg"
done

# 5. Verify final content matches original (reformatted)
git show <original-HEAD>:<file> > /tmp/orig
<formatter> /tmp/orig
diff /tmp/orig <file>  # should be empty

# 6. Update the original branch
git branch -f <original-branch> HEAD
git checkout <original-branch>
git branch -D temp-branch

Why this works: each commit's complete file state comes from the original branch (where it was correct) and is reformatted — reconstruct, don't merge. The formatter being idempotent is what makes it safe to run unconditionally in the loop: re-running it on already-formatted code is a no-op.

Moving File Changes Between Commits

Checkout-and-reconstruct. When a commit contains changes to files that belong in different commits (e.g., a production code fix committed together with test updates that belong in the next commit), reconstruct the history by checking out specific file states from the old commits.

1. Check out the commit before the one to split

git checkout <parent-of-commit-to-split>

2. Rebuild the first commit with only the files it should contain

git checkout <original-commit> -- path/to/file_A
git commit -m "First commit message"

3. Rebuild the next commit by combining leftover files with its own files

git checkout <original-commit> -- path/to/file_B       # leftover from split
git checkout <next-commit> -- path/to/file_C file_D    # files from next commit
git commit -m "Second commit message"

git checkout <sha> -- <file> grabs a file's exact state from any commit and stages it — the mechanism behind reconstruct-don't-merge, here recombining file changes across commits without patches or interactive rebase.

4. Cherry-pick remaining commits

git cherry-pick <remaining-commit-1> <remaining-commit-2> ...

5. Point the branch at the new history and verify

git branch -f <branch> HEAD
git checkout <branch>
git diff <branch>_backup..<branch> --stat   # should be empty

Splitting One Working-Tree Change Across Multiple Fixup Targets

Per-slice fixups. Unlike the section above (which recombines existing commits), this covers the common case where you have one uncommitted edit to a file that must land in multiple historical commits — one fixup per target, each carrying only its slice.

Example: you've edited output.py to (a) add a HASH_LENGTH constant (belongs in the commit that introduced hashing), (b) harden the filename sanitizer (belongs in the sanitization commit), and (c) replace the tmp-file write with O_NOFOLLOW/O_EXCL (belongs in the atomic-write commit).

# 1. Save the final state and reset the file to HEAD
cp src/output.py /tmp/output.final
git checkout HEAD -- src/output.py

# 2. Apply ONLY the slice for target A (the hashing commit).
#    Hand-edit src/output.py to introduce HASH_LENGTH and its usages.
$EDITOR src/output.py
git add src/output.py
git commit -m "fixup! <subject of hashing commit>"

# 3. Apply slice B (the sanitizer commit). Re-edit to add the
#    control-char / bidi / NAME_MAX cap changes.
$EDITOR src/output.py
git add src/output.py
git commit -m "fixup! <subject of sanitization commit>"

# 4. Apply slice C (the atomic-write commit). Re-edit to add
#    O_NOFOLLOW / O_EXCL / unique tmp suffix.
$EDITOR src/output.py
git add src/output.py
git commit -m "fixup! <subject of atomic-write commit>"

# 5. Verify the cumulative result matches the saved final state
diff /tmp/output.final src/output.py  # should be empty

# 6. Autosquash
GIT_SEQUENCE_EDITOR=true git rebase -i --autosquash <base>

Why this works: each fixup carries only the slice valid against its target's state, so the rebase applies each on top of a file that already has everything before it — reconstruct, don't merge, at the per-slice level.

Common pitfall: committing the entire current file state under a fixup-A message just because A is the file's earliest commit. The fixup then carries content (symbols, imports, functions) that doesn't exist at A and will conflict, often noisily, when the rebase replays it.

Shortcut: mechanical transformations via git rebase --exec

When the slice is a mechanical, idempotent transformation (sed rename, ruff format, codemod), you don't need to hand-edit per-slice — git rebase --exec does the slicing automatically:

git rebase --exec '<transformation>; if ! git diff --quiet <file>; then git add <file> && git commit --amend --no-edit; fi' <base>

After each pick, the exec runs the transformation, and --amend folds any resulting change into the just-picked commit. Because at each pick the only <file> content "new" relative to the previous pick is what that commit contributed, the transformation naturally slices itself across the chain. Commits that don't touch <file> (or touch it without producing a diff after the transformation) skip the amend silently.

Concrete example — folding a global rename <old_name> → <new_name> into the three commits that introduced those references:

git rebase --exec 'sed -i "s/<old_name>/<new_name>/g" <file>; if ! git diff --quiet <file>; then git add <file> && git commit --amend --no-edit; fi' <earliest-introducing-commit>^

After the rebase, each of the three commits' diff shows <new_name> as if it had been written that way originally. No follow-up "fix: rename …" commit is needed; no hand-editing per slice.

Use this when: the transformation is monotonic and you want it folded into whichever commits introduced the affected lines. Typical fits: global identifier renames, formatter runs after the fact, codemods.

Don't use this when:

• The right slice differs from the mechanical one (e.g. some occurrences should be renamed, others kept — the transformation would over-apply).
• The transformation is not idempotent — re-running it should be a no-op, otherwise the amend will re-trigger on already-transformed commits and noise up history.
• The transformation depends on context outside the touched file (e.g. needs imports that this commit hasn't introduced yet) — that's a per-slice judgment call, not a mechanical apply.

Downstream chain caveat: rewriting commits in this branch changes their SHAs, so any branch stacked on top must be re-rebased afterward (git rebase --onto <new-tip> <old-tip> <downstream-branch>). Snapshot the old tips into tags (git tag old/<branch> <sha>) before the rewrite so the upstreams remain referenceable.

Diagnosing Autosquash Conflicts

When autosquash stops with a conflict, the conflict marker almost always reveals which mistake you made. Read the >>>>>>> block — the "theirs" side — and compare it against the file state at the current pick:

• Your fixup adds a symbol (constant, function) that doesn't exist in the surrounding file yet, or references an import (os, Path, etc.) the file doesn't have yet. The fixup is targeting a commit earlier than where that symbol or import is naturally introduced. Fix: keep HEAD, then carve the offending lines into a separate fixup against the later commit.
• Your fixup deletes or wholesale-replaces a function that a later branch commit also modifies. The later commit will conflict against an empty or changed target when its turn comes. Fix: accept HEAD when the later commit conflicts; it shrinks to whatever changes still apply, or empties out.
• Your fixup touches lines that another fixup against a later commit also touches. Two fixups are racing for the same lines. Fix: order matters — the later-targeted fixup should be a no-op against the already-modified lines, or its slice needs to be redrafted.
• Conflict markers appear in a file you didn't intend to touch. A merge-recursive 3-way pulled in collateral changes. Fix: resolve to HEAD, verify with git diff HEAD -- <file> after, and run git rebase --skip only if the resulting commit is truly empty.

General rule: if you can't immediately explain which target commit each conflicting line belongs to, abort with git rebase --abort, re-audit per-file targets, and split the offending fixup.

Common Mistakes

Mistake	Fix
Writing a custom sequence editor instead of using --autosquash	Use GIT_SEQUENCE_EDITOR=true git rebase -i --autosquash <base>
Inserting a reflog SHA manually into the todo file	Re-create the commit in the branch, then autosquash
Not verifying the result	Always run git show <sha> --stat after rebasing
Single-pass sequence editor script	Two passes: collect first, emit second
Assuming "rebase succeeded" means it did the right thing	Verify with git show
Cherry-picking code commits onto a reformatted base	Use the replay-and-reformat pattern (see above) — cherry-pick produces dozens of unsolvable formatting conflicts
Using interactive rebase (-i) to split/rearrange commits	Claude Code can't use -i; use the checkout-and-reconstruct pattern instead
Lumping all of a file's edits into one fixup when the file appears in multiple branch commits	Audit per-file targets up front; split the diff into one fixup per target — see "Splitting One Working-Tree Change Across Multiple Fixup Targets"
Batching many fixups before a single autosquash on a long branch	Commit one fixup, autosquash, verify, repeat — conflicts surface at the source instead of mid-rebase
Treating an autosquash conflict as a merge problem to resolve in place	The conflict is usually telling you a fixup spans the wrong number of target commits; abort, split, retry