[BUG] False-positive inode deduplication prevents custom agents and skills from loading

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Custom agents in .claude/agents/ and skills in .claude/skills/ are incorrectly being skipped with "same inode already loaded" errors, even though all files have unique inodes and are not symlinks or hard links.

Environment:

• Claude Code version: 2.1.2
• OS: Linux (WSL2) 6.5.0-45-generic
• Platform: linux

Impact:

• 7 of 14 skills not loading
• 5 of 9 agents not loading

Debug Log Output (~/.claude/debug/latest):

  2026-01-09T10:09:15.110Z [DEBUG] Skipping duplicate skill 'review:worktree' from projectSettings (same inode already loaded from projectSettings)
  2026-01-09T10:09:15.110Z [DEBUG] Skipping duplicate skill 'manager:agent' from projectSettings (same inode already loaded from projectSettings)
  2026-01-09T10:09:15.110Z [DEBUG] Skipping duplicate skill 'manager:plan' from projectSettings (same inode already loaded from projectSettings)
  2026-01-09T10:09:15.110Z [DEBUG] Skipping duplicate skill 'review:agent' from projectSettings (same inode already loaded from projectSettings)
  2026-01-09T10:09:15.110Z [DEBUG] Skipping duplicate skill 'manager:command' from projectSettings (same inode already loaded from projectSettings)
  2026-01-09T10:09:15.110Z [DEBUG] Skipping duplicate skill 'git:worktree' from projectSettings (same inode already loaded from projectSettings)
  2026-01-09T10:09:15.110Z [DEBUG] Skipping duplicate skill 'implement' from projectSettings (same inode already loaded from projectSettings)
  2026-01-09T10:09:15.110Z [DEBUG] Deduplicated 7 skills (same inode)

  2026-01-09T10:09:15.154Z [DEBUG] Skipping duplicate file '.../agent-manager.md' from projectSettings (same inode already loaded from projectSettings)
  2026-01-09T10:09:15.154Z [DEBUG] Skipping duplicate file '.../implementation-plan-reviewer.md' from projectSettings (same inode already loaded from projectSettings)
  2026-01-09T10:09:15.154Z [DEBUG] Skipping duplicate file '.../command-reviewer.md' from projectSettings (same inode already loaded from projectSettings)
  2026-01-09T10:09:15.154Z [DEBUG] Skipping duplicate file '.../implementation-planner.md' from projectSettings (same inode already loaded from projectSettings)
  2026-01-09T10:09:15.154Z [DEBUG] Skipping duplicate file '.../research-agent.md' from projectSettings (same inode already loaded from projectSettings)
  2026-01-09T10:09:15.154Z [DEBUG] Deduplicated 5 files in agents (same inode via symlinks or hard links)

Proof of Unique Inodes (Skills):
$ ls -li .claude/skills/*/SKILL.md

   8608374769736089602  git:clean-gone/SKILL.md      # LOADING ✓
   1013607562425729026  git:reset-main/SKILL.md      # LOADING ✓
  13654077056950861826  git:worktree/SKILL.md        # NOT LOADING
  10932640812901400578  implement/SKILL.md           # NOT LOADING
  15721616442062733314  manager:agent/SKILL.md       # NOT LOADING
  15676015094244376578  manager:command/SKILL.md     # NOT LOADING
  15428137315299753986  manager:plan/SKILL.md        # NOT LOADING
   6959267567866085378  research/SKILL.md            # LOADING ✓
  17961712405993750530  review:agent/SKILL.md        # NOT LOADING
   8851112614497353730  review:command/SKILL.md      # LOADING ✓
  15119287221347221506  review:plan/SKILL.md         # LOADING ✓
   6473542763894276098  review:research/SKILL.md     # LOADING ✓
  16775286845953343490  review:worktree/SKILL.md     # NOT LOADING
   7785136332803932162  session:handover/SKILL.md    # LOADING ✓

Proof of Unique Inodes (Agents):
$ ls -li .claude/agents/*.md

  12488223444701347842  agent-manager.md               # NOT LOADING
   8222780255991169026  agent-reviewer.md              # LOADING ✓
  16335656929880899586  command-manager.md             # LOADING ✓
  14847734174311645186  command-reviewer.md            # NOT LOADING
   9090508994217443330  implementation-executor.md     # LOADING ✓
  16956450589226958850  implementation-planner.md      # NOT LOADING
  15700323371469504514  implementation-plan-reviewer.md # NOT LOADING
  17179524646823723010  research-agent.md              # NOT LOADING
   1565241084012920834  session-manager.md             # LOADING ✓

Workarounds Attempted:

• Cache clearing (rm -rf ~/.claude/cache/*) - did not fix
• Manual Task tool invocation - fails, agents not available
• All files verified to have correct permissions and valid YAML frontmatter

What Should Happen?

I should be able to use agents and skills I created.

Error Messages/Logs

 Let me try invoking one of the "missing" agents directly.

● agent-manager(Test agent-manager invocation)
  ⎿  Initializing…
  ⎿  Error: Agent type 'agent-manager' not found. Available agents: Bash, general-purpose, statusline-setup, Explore, Plan, claude-code-guide, implementation-executor, 
     command-manager, session-manager, agent-reviewer

Steps to Reproduce

I have no idea, upgraded Claude and things stopped working.

Claude Model

Used Sonet and Opus - same problem.

Is this a regression?

Yes, this worked in a previous version

Claude Code Version

2.1.2

Platform

Anthropic API

Operating System

Other Linux

Terminal/Shell

VS Code integrated terminal