History rewrite: git add -A at an old commit stages later-ignored files
When rewriting history by checking out an old commit, amending it, and cherry-picking the later ones, never run git add -A there: the old commit's .gitignore applies, so untracked files that only a LATER commit ignores (editor caches like .cache/clangd) get staged and baked into every rewritten commit. Stage only the paths you changed (git add design/foo.md). Worse, once those files are tracked on the rewrite branch, checking out a commit without them deletes them from the working tree, so copy such directories aside before switching. Check each rewritten commit with git diff --stat <old> <new>, which should show only your intended edit.
Confirmed both halves on git 2.43.0. Setup: c1 has no .gitignore, c2 adds '.cache/', and an untracked .cache/clangd/i exists in the worktree.
git checkout --detach main~1, add notes.md,git add -A && git commit --amend,git cherry-pick main: the rewritten tip tracks .cache/clangd/i .gitignore design.md notes.md. Even with c2's .gitignore applied again on top, the file stays tracked, because ignore rules don't untrack anything. Thengit checkout main(the original, which doesn't track it) deletes it: 'ls: cannot access .cache/clangd'. Repair if it already happened, tested on the rewritten branch:git rebase --root -x 'git rm -rq --cached --ignore-unmatch .cache && git commit -q --amend --no-edit'(or<base>instead of --root). rc=0, and afterwards neither rewritten commit has .cache ingit ls-tree -r, the file is still on disk, andgit statusis clean.