claude-code - 💡(How to fix) Fix [BUG] isolation: "worktree" corrupts origin remote URL and injects partial clone settings into .git/config

Summary

The repository's origin remote was corrupted: the URL changed from [email protected]:org/myrepo.git to https://github.com/ruby/gem_rbs_collection.git, and partial clone settings (promisor = true, partialclonefilter = blob:none) were injected along with duplicate fetch entries. As a result, git push failed with "Permission denied" and git fetch was pulling branches from an unrelated repository.

Timeline

Evidence

Resulting .git/config remote section:

[remote "origin"]
    url = https://github.com/ruby/gem_rbs_collection.git
    fetch = +refs/heads/*:refs/remotes/origin/*
    fetch = +refs/heads/*:refs/remotes/origin/*
    promisor = true
    partialclonefilter = blob:none
    fetch = +refs/heads/*:refs/remotes/origin/*
    fetch = +refs/heads/*:refs/remotes/origin/*
    fetch = +refs/heads/*:refs/remotes/origin/*

The config also contains a [branch "worktree-user+test"] entry with remote = origin and merge = refs/heads/main, auto-generated by Claude Code.

Full corrupted .git/config at time of detection:

[core]
    repositoryformatversion = 0
    filemode = true
    bare = false
    logallrefupdates = true
    ignorecase = true
    precomposeunicode = true
    hooksPath = /Users/user/projects/myrepo/.git/hooks
[remote "origin"]
    url = https://github.com/ruby/gem_rbs_collection.git
    fetch = +refs/heads/*:refs/remotes/origin/*
    fetch = +refs/heads/*:refs/remotes/origin/*
    promisor = true
    partialclonefilter = blob:none
    fetch = +refs/heads/*:refs/remotes/origin/*
    fetch = +refs/heads/*:refs/remotes/origin/*
    fetch = +refs/heads/*:refs/remotes/origin/*
...
[branch "worktree-user+test"]
    remote = origin
    merge = refs/heads/main

Root cause (hypothesis)

Evidence strongly points to Claude Code's isolation: "worktree" feature as the origin of the corruption. A git bug cannot be ruled out entirely, but is considered unlikely.

Evidence pointing to Claude Code

• The branch worktree-user+test is clearly auto-generated — the user created -b test, not that name. It was created on April 17 from origin/main and has a commit authored by Claude Code.
• The EnterWorktree tool is available in Claude Code sessions and is part of the isolation: "worktree" implementation.
• The promisor = true and partialclonefilter = blob:none settings are characteristics of a partial clone — a technique Claude Code likely uses to create lightweight worktrees.

Probable sequence

1. April 17: Claude Code ran an agent with isolation: "worktree", which invoked EnterWorktree. As part of its fetch mechanism, it configured origin with the wrong URL (gem_rbs_collection) and partial clone parameters, and created the worktree-user+test branch.

2. April 20, 12:01: The user manually created the test worktree. git worktree add itself does not modify remotes.

3. April 20, 12:09–12:10: A subsequent operation (possibly Claude Code re-invoking EnterWorktree, a fetch triggered by a devcontainer init script, or an IDE running git operations when opening the devcontainer) ran git fetch origin against the already-corrupted remote, updating FETCH_HEAD with gem_rbs_collection branches and consolidating the corruption in the config.

Why gem_rbs_collection

Unknown. Possible causes:

• Bug in Claude Code when resolving the remote URL during worktree creation.
• Confusion between the project remote and the gem_rbs_collection repository, which is a Ruby RBS type definitions collection — a dev dependency of the project's Ruby stack.

Ruled out: git bug

git worktree add is a local operation that does not modify remotes. All repository hooks are .sample files (inactive). git 2.50.1 (Apple Git-155) has no known bugs related to this operation.

Impact

• git push failed with remote: Permission to ruby/gem_rbs_collection.git denied to username.
• git fetch was pulling branches from an unrelated external repository.
• No commits or project data were lost (local history was not affected).

Fix

Restore [remote "origin"] in .git/config:

[remote "origin"]
    url = [email protected]:org/myrepo.git
    fetch = +refs/heads/*:refs/remotes/origin/*

Environment

• OS: macOS Darwin 25.4.0
• git: 2.50.1 (Apple Git-155)
• Claude Code: CLI, model claude-sonnet-4-6
• Project structure: monorepo with git worktrees stored under .claude/worktrees/
• Active hooks: none (all .sample)

Related issues

• anthropics/claude-code#45201 — isolation: "worktree" also modifies .git/config (sets extensions.worktreeConfig), confirming the feature writes to the shared config as a side effect.
• anthropics/claude-code#47266 — concurrent worktree creation causes .git/config lock collisions, further evidence that the feature performs direct writes to .git/config.