[BUG] git-subdir plugin install leaks sparse-checkout into the session's working repo, silently collapsing the tree

Summary

Installing or refreshing a plugin whose marketplace source is git-subdir runs git sparse-checkout set --cone <path> that is not scoped to its temp clone — it also applies to the git repository at the session's current working directory. That sets core.sparseCheckout=true plus a cone pattern for the plugin's subpath (e.g. providers/claude/plugin) on the user's own project worktree, so every file outside that (nonexistent-in-this-repo) path silently disappears from the working tree. No error is shown.

Impact

• The user's working tree collapses — src/, .claude/, etc. vanish, with exit-0 git behavior. It looks like data loss / a broken checkout.
• While sparse-checkout is active, a plain git add <path> silently refuses to stage paths outside the cone (it's only a hint, exit stays 0), so a subsequent git commit --amend / push can ship incomplete content without warning.
• Hits multi-worktree tooling (Conductor, plain git worktree) hardest, because the session cwd is a real repo. It recurs on every marketplace re-sync.

Environment

• Claude Code v2.1.156
• macOS 26.3.1 (Darwin 25.3.0), Apple Silicon
• Trigger plugin: stripe@claude-plugins-official, source:

``json
{"source":"git-subdir","url":"https://github.com/stripe/ai.git","path":"providers/claude/plugin","ref":"main","sha":"a34795211da530a168f581122011bb5ceb2e4bd0"}
``

• Sessions running inside Conductor-managed git worktrees of an unrelated project.

Reproduction

1. Open a project in Claude Code where the working directory is a git repo / worktree.
2. Install (or let the official marketplace auto-refresh) a plugin with a git-subdir source that points at a subpath of an external monorepo — e.g. stripe@claude-plugins-official (github.com/stripe/ai → providers/claude/plugin).
3. Inspect the project repo (not the plugin cache):

• git config core.sparseCheckout → true
• <git-dir>/info/sparse-checkout now contains a cone pattern for providers/claude/plugin — a path that does not exist in the project.

1. All files outside that path are gone from the working tree.

Evidence

• The polluting <project-worktree>/.git/.../info/sparse-checkout is byte-identical to the plugin's temp clone at ~/.claude/plugins/cache/temp_subdir_*.clone/.git/info/sparse-checkout — i.e. the same git sparse-checkout operation wrote both.
• Only repositories that were the session cwd during a git-subdir install/refresh are affected. The plugin's own temp clone is correct. Other source types never touch sparse-checkout and never leak:
• source: "./plugins/<name>" (a subfolder of the already-cloned marketplace repo) → no fetch, no sparse.
• whole-repo github/url sources → plain clone, no sparse.
• Reproduced across three separate worktrees of the same project; never affected the non-Conductor main checkout (which wasn't a session cwd when a git-subdir install ran).

Root cause (inferred — harness is closed source)

The git-subdir fetch path's git sparse-checkout invocation runs against the inherited process working directory instead of being confined to the temp clone directory.

Suggested fix

Scope every git operation in the git-subdir fetch to the temp clone directory — e.g. git -C <tempCloneDir> sparse-checkout … (or set the child process cwd to the temp dir) — so a plugin install can never mutate the user's working repository. Optionally assert the target repo is the temp dir before running sparse-checkout.

Workaround

In the affected repo:

git sparse-checkout disable
rm -f "$(git rev-parse --git-dir)/info/sparse-checkout"

Recurs on the next marketplace refresh until fixed.

Related

• #58199 — git-subdir install creates an empty destination directory. Same install path, different symptom; suggests this code path is fragile.
• #40864 / #28426 — the "use sparse checkout for plugin installs" feature this mis-scopes.