[BUG] Duplicate slash commands when ~/.claude is symlinked to dotfiles directory (regression of #2316 in v2.0.36)

Description

Custom slash commands are displayed twice in the command list when ~/.claude is a directory symlink to a dotfiles repository. Each command appears with two different labels: (project) and (project, gitignored).

Environment

• OS: macOS 26.0.1 (Darwin 25.0.0, Build 25A362)
• Claude Code version: 2.0.36
• Setup: ~/.claude → ~/.dotfiles/.claude (directory symlink)

Steps to Reproduce

1. Create a dotfiles directory structure:

``
~/.dotfiles/.claude/
├── commands/
│ ├── commit.md
│ ├── pr.md
│ └── save-context.md
├── settings.json
└── settings.local.json
``

1. Create a directory symlink:

``bash
ln -s ~/.dotfiles/.claude ~/.claude
``

1. Launch Claude Code from any directory (not just home directory)

1. Type / to open the command list

1. Observe duplicate entries for each custom command

Expected Behavior

Each custom command should appear only once in the command list.

Actual Behavior

Each custom command appears twice with different labels:

• First occurrence: labeled as (project)
• Second occurrence: labeled as (project, gitignored)

Example output:

/commit    変更内容を確認し、適切な粒度でコミットを作成する (project)
/commit    変更内容を確認し、適切な粒度でコミットを作成する (project, gitignored)
/pr        効率的にPR作成（変更分析、title/body生成、レビュアー自動指定） (project)
/pr        効率的にPR作成（変更分析、title/body生成、レビュアー自動指定） (project, gitignored)

Additional Context

• This issue occurs in all directories, not just when running from the home directory
• Issue #2316 reported a similar problem that was fixed in v1.0.61, suggesting this may be a regression
• The physical file location is the same (confirmed via readlink -f), but Claude Code appears to register it twice through different paths
• Commands are functional despite being duplicated

Related Issues

• #2316 - Similar duplication issue, marked as fixed in v1.0.61
• #10573 - Symlink detection issue (different problem: commands not detected at all)