How to fix You need to fix your working tree before running bisect in Git

First, see exactly what changes are preventing bisect:

git status

This shows:
- Changes not staged for commit: Modified tracked files
- Changes to be committed: Staged changes waiting for commit
- Untracked files: New files Git doesn't know about

Identify which category your changes fall into before proceeding.

The safest option is to stash your changes, which saves them temporarily:

git stash push -m "WIP: changes before bisect"

This saves both staged and unstaged changes. After bisect completes, restore them:

git stash pop

Include untracked files if needed:

git stash push -u -m "WIP: all changes before bisect"

The -u flag includes untracked files in the stash.

Now that your working tree is clean, begin bisecting:

git bisect start
git bisect bad HEAD              # Current commit has the bug
git bisect good <known-good-commit>  # Replace with a commit hash or tag

Git will checkout a commit halfway between good and bad. Test it, then mark:

git bisect good   # If this commit doesn't have the bug
# OR
git bisect bad    # If this commit has the bug

Repeat until Git identifies the first bad commit.

When bisect finds the problematic commit, it displays the result. End the session:

git bisect reset

This returns your repository to the branch you were on before bisecting. Now restore your stashed changes:

git stash pop

If you have multiple stashes, list them first:

git stash list
git stash pop stash@{0}  # Apply specific stash

If your changes are substantial, commit them to a temporary branch instead of stashing:

git checkout -b temp-work-branch
git add .
git commit -m "WIP: temporary commit for bisect"
git checkout main  # or your original branch

After bisecting:

git checkout temp-work-branch
git reset HEAD~1   # Undo the commit, keep changes
git checkout main
git branch -D temp-work-branch  # Clean up

If you don't want to interrupt your current work at all, create a separate working directory:

git worktree add ../bisect-worktree HEAD
cd ../bisect-worktree
git bisect start
git bisect bad HEAD
git bisect good <known-good-commit>

This creates a linked working tree where you can bisect independently. Your main working directory remains untouched.

Clean up after bisecting:

cd ..
rm -rf bisect-worktree
git worktree prune

If a previous bisect session wasn't cleaned up properly:

git bisect reset

If that fails, manually remove bisect state:

rm -rf .git/BISECT_*
git checkout <your-branch>

Then stash/commit your changes and start fresh.