Global commands from ~/.claude/commands/ not appearing in slash command menu

Description

Custom global commands in ~/.claude/commands/ are not appearing in the slash command menu (either via / filter or the + → "Slash commands" UI). Only two plugin-provided skills (schedule and btw) appear. All plugin skills show correctly under the Plugins submenu.

Environment

• Claude Code version: 2.1.110
• Platform: macOS (Darwin 25.3.0), Claude Code Desktop app
• Plugins enabled: ~35 (see list below)
• MCP connectors: ~20 enabled

Steps to Reproduce

1. Have 16 properly formatted .md command files in ~/.claude/commands/ (with YAML frontmatter including description field)
2. Have many plugins enabled in settings.json (enabledPlugins)
3. Type / in the input box — only schedule and btw appear (both from plugins)
4. Click + → "Slash commands" — only plugin skill categories are listed, no global commands

Expected Behavior

Global commands from ~/.claude/commands/ (e.g., commit, session-start, session-end, checkpoint, etc.) should appear in the / menu alongside plugin skills.

Actual Behavior

• / filter shows only 2 items: schedule and btw (both plugin skills)
• + → "Slash commands" shows only plugin skill categories (Operations, PDF viewer, Human resources, Design, Brand voice, etc.)
• No custom global commands appear anywhere in the UI
• This was working previously — regression at some point

Command Files (all valid)

~/.claude/commands/
├── checkpoint.md
├── commit.md
├── debrief.md
├── monthly-review.md
├── obsidian-sync.md
├── orchestrate.md
├── plan-master.md
├── prep.md
├── prettygithub.md
├── ready-to-build.md
├── research-bookmarks.md
├── roadmap-with-validation.md
├── session-end.md
├── session-start.md
└── greenhouse/
    └── (subcommands)

Example frontmatter (commit.md):

---
description: Smart commit - run tests, generate message, commit
---

Enabled Plugins

superpowers, commit-commands, plugin-dev, claude-md-management, claude-code-setup, feature-dev, code-review, code-simplifier, pr-review-toolkit, agent-sdk-dev, frontend-design, ralph-loop, hookify, skill-creator, playground, vercel, slack, stripe, explanatory-output-style, learning-output-style, imessage, codex, rust-analyzer-lsp, typescript-lsp, pyright-lsp, playwright, supabase, linear, greptile, github, huggingface-skills, context7

Hypothesis

With many plugins enabled, plugin skill discovery may be suppressing or replacing global command discovery entirely. Several plugin skills share names with global commands (e.g., commit, session-start, session-end), which may contribute to the issue.