[BUG] CLAUDE.md and .claude/rules/ loaded twice in git worktrees

Description

When running Claude Code inside a git worktree, project instructions (CLAUDE.md, AGENTS.md, .claude/rules/*.md) are loaded twice — once from the worktree path and once from the main repository path. Both copies appear in the system context, doubling the context usage for project instructions.

Reproduction steps

1. Have a repo with CLAUDE.md and/or .claude/rules/ containing project instructions
2. Create a git worktree:

``bash
git worktree add .worktrees/my-feature -b my-feature
``

1. Open Claude Code in the worktree directory:

``bash
cd .worktrees/my-feature
claude
``

1. Observe the loaded context — every project instruction file appears twice:

• Contents of /path/to/main-repo/CLAUDE.md
• Contents of /path/to/main-repo/.worktrees/my-feature/CLAUDE.md
• Contents of /path/to/main-repo/.claude/rules/frontend.md
• Contents of /path/to/main-repo/.worktrees/my-feature/.claude/rules/frontend.md

Expected behavior

Each project instruction file should be loaded exactly once, regardless of whether running in a worktree or the main repo.

Actual behavior

Every file from CLAUDE.md, AGENTS.md, and .claude/rules/ is loaded twice. Both copies contain identical content since they are the same files in the same git repository.

Root cause

Same as #26992. In a git worktree, .git is a file pointing back to the main repo:

gitdir: /path/to/main-repo/.git/worktrees/<name>

Claude Code discovers project instructions from both:

1. The worktree's CWD (e.g., .worktrees/my-feature/CLAUDE.md)
2. The main repository root (by following .git back to the main repo, e.g., main-repo/CLAUDE.md)

Since both paths resolve to the same git content, every instruction file appears twice.

Suggested fix

• Deduplicate discovered files by inode or content hash
• Or resolve both paths to the same canonical git root and only load once
• Or detect worktree context and only load from the CWD path

Environment

• Claude Code version: 2.1.47
• OS: macOS (Darwin 25.0.0)
• Shell: zsh

Related issues

• #26992 — Same root cause, but for duplicate slash commands in worktrees
• #27069 — Duplicate skills/commands in worktrees