fix(cli): preserve .git directory when scaffolding into a non-empty folder

[itsjustriley]

WHY are these changes introduced?

Fixes dt#1201 · Closes #2989

Running npm create @shopify/hydrogen@latest in a directory that already contains a git repo wipes out the .git/ folder, taking the entire commit history with it. People hit this when they want to start with a blank repo + README and scaffold Hydrogen on top — a pretty common way to start a project.

The usual workaround is to mv .git ../tmp-git, scaffold, then move it back. That's fragile, not obvious, and nobody should have to think about it.

WHAT is this pull request doing?

When the CLI clears a non-empty target directory during scaffolding, it now skips .git/ (both directory and gitfile forms). Everything else is deleted as before.

Two small copy updates so users know what's happening:

• Confirmation prompt: "The directory X is not empty. Continuing will delete its contents (your .git directory is kept). Continue?"
• Declined-confirmation hint: "You may use --force or -f to delete its contents (.git is always preserved)."

A few deliberate scope choices:

• No new flag. Preserving .git/ is the right default; an opt-in --preserve-git flag would just be surface area nobody sets correctly.
• Only .git/ is carved out. .gitignore, .env, and .shopify/ are legitimate scaffold-owned files, so they're deleted as before.
• Both @shopify/cli-hydrogen and @shopify/create-hydrogen bumped. Per CLAUDE.md, changes to the init command path require both packages to be bumped so new scaffolds pick up the fix.

HOW to test your changes?

Everything below runs in a throwaway $TMPDIR directory. Your real .git folders outside the sandbox are never touched.

Setup (once):

git fetch origin fix/cli-preserve-git-on-scaffold
git checkout fix/cli-preserve-git-on-scaffold
pnpm install
pnpm --filter @shopify/cli-hydrogen build
pnpm --filter @shopify/create-hydrogen build

export HYDROGEN_BIN="$PWD/packages/create-hydrogen/dist/create-app.js"
export SANDBOX=$(mktemp -d -t hydrogen-tophat.XXXXXX)

---

Scenario 1 — the bug (non-empty dir with existing .git):

cd "$SANDBOX" && mkdir repo-a && cd repo-a
git init -q
git config user.email you@example.com
git config user.name You
echo "pre-existing" > README.md
mkdir src && echo "// old" > src/app.js
git add -A && git commit -q -m "Pre-existing project"

# Answer YES at the prompt
node "$HYDROGEN_BIN" --path . --mock-shop --language ts \
  --styling tailwind --markets none --no-install-deps --no-shortcut

What to check:

• Confirmation prompt reads "…your .git directory is kept".
• .git/ still exists after the scaffold.
• git log --oneline shows both your "Pre-existing project" commit and the new "Scaffold Storefront" commit on top.
• src/app.js is gone (not part of the skeleton); README.md is now the skeleton's README.

---

Scenario 2 — decline the prompt:

cd "$SANDBOX" && mkdir repo-b && cd repo-b
git init -q
echo keepme > keepme.txt

# Answer NO at the prompt
node "$HYDROGEN_BIN" --path . --mock-shop --language ts \
  --styling tailwind --markets none --no-install-deps --no-shortcut

What to check:

• The info message after declining includes ".git is always preserved".
• keepme.txt and .git/ both survive.

---

Scenario 3 — --force path (no prompt, still preserves .git):

cd "$SANDBOX" && mkdir repo-c && cd repo-c
git init -q
git config user.email you@example.com
git config user.name You
echo existing > README.md
git add -A && git commit -q -m "Pre-existing (force)"
OLD=$(git rev-parse HEAD)

node "$HYDROGEN_BIN" --path . --force --mock-shop --language ts \
  --styling tailwind --markets none --no-install-deps --no-shortcut

git cat-file -e "$OLD" && echo "original commit still reachable ✓"

What to check:

• No prompt appears.
• .git/ exists.
• Original commit hash is still reachable.

---

Cleanup:

rm -rf "$SANDBOX"
unset HYDROGEN_BIN SANDBOX

Empty directories and non-empty directories without .git/ are covered by automated tests in packages/cli/src/lib/onboarding/common.test.ts, so no need to tophat those manually.

Checklist

• I've read the Contributing Guidelines
• I've considered possible cross-platform impacts (Mac, Linux, Windows)
• I've added a changeset if this PR contains user-facing or functional changes. Test changes or internal-only config changes do not require a changeset.
• I've added tests to cover my changes
• I've added or updated the documentation

[shopify]

Oxygen deployed a preview of your fix/cli-preserve-git-on-scaffold branch. Details:

Storefront	Status	Preview link	Deployment details	Last update (UTC)
Skeleton (skeleton.hydrogen.shop)	✅ Successful (Logs)	Preview deployment	Inspect deployment	April 22, 202610:12 AM

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