Skills broken in 2.1.88, work correctly in 2.1.87

Summary

Custom skills (.claude/skills/*/SKILL.md) stopped working after upgrading from 2.1.87 to 2.1.88. Downgrading to 2.1.87 restores full functionality. The issue is 100% reproducible across multiple repos on the same machine.

Environment

• Claude Code version: 2.1.88 (broken), 2.1.87 (working)
• OS: macOS 26.3 (Darwin 25.3.0, arm64, Apple Silicon Mac Mini)
• Node: v20.20.1
• Shell: zsh

Reproduction

1. Install Claude Code 2.1.87 — skills work correctly
2. Upgrade to 2.1.88 — skills stop working
3. Downgrade to 2.1.87 — skills work again

No changes to skill files, settings, or project structure between versions. The only variable is the Claude Code version.

Skills Configuration

Skills are defined at three levels, all affected:

User-level (~/.claude/skills/)

• 3 skills (finishing-branches, reviewing-and-fixing, running-sprint-tasks)

Project-level (.claude/skills/)

• 11-14 skills per repo (architecting-modules, auditing-sibling-projects, capturing-corrections, creating-skills, designing-and-implementing, drafting-content, finishing-branches, implementing-with-tdd, managing-task-lifecycle, planning-with-trello, releasing-versions, reviewing-code, running-qc)
• Skill files range from 70 to 392 lines
• Total across all skills: ~4,465 lines

Skill file format (standard SKILL.md with frontmatter)

---
name: planning-with-trello
description: Manages feature planning workflow including budget validation, task creation, and Trello synchronization.
skills: [planning-with-trello]
agent-roles: [navigator]
---

# Planning with Trello
...

Hooks Configuration (.claude/settings.json)

Active hooks that may interact with skill loading:

{
  "hooks": {
    "PreToolUse": [
      {
        "matcher": "Edit|Write",
        "hooks": [
          { "type": "command", "command": "bpsai-pair enforce task-edit ..." },
          { "type": "command", "command": "bpsai-pair enforce state-edit ..." }
        ]
      }
    ],
    "UserPromptSubmit": [
      { "hooks": [{ "type": "command", "command": "bpsai-pair session check --quiet" }] }
    ],
    "PreCompact": [
      { "hooks": [{ "type": "command", "command": "bpsai-pair compaction snapshot save ..." }] }
    ],
    "PostToolUse": [
      {
        "matcher": "Edit|Write",
        "hooks": [{ "type": "command", "command": "bpsai-pair history-log --quiet" }]
      }
    ]
  }
}

Observed Behavior

On 2.1.87: Skills appear in the system-reminder skills list, /skill-name slash commands work, Skill tool invocations succeed, skill descriptions appear in the model's available skills.

On 2.1.88: Skills do not function. The exact failure mode from the user's perspective is that invoking skills (either via /skill-name or via the Skill tool) does not work as expected.

Tested Across Multiple Repos

This issue reproduces across at least two independent repos on the same machine:

1. ~/ops — 14 project-level skills
2. ~/projects/stay-at-home — 11 project-level skills

Both repos have identical skill file formats (SKILL.md with YAML frontmatter). Both work on 2.1.87, both break on 2.1.88.

Workaround

Downgrade to 2.1.87:

npm install -g @anthropic-ai/claude-code@2.1.87

Expected Behavior

Skills defined in .claude/skills/*/SKILL.md should load and function identically in 2.1.88 as they do in 2.1.87.