Claude Code `/plugin` warns that root `commands/` (Antigravity) folder is ignored

[hyhmrright]

Summary

When agent-skills is installed as a Claude Code plugin, the /plugin manager shows a warning that the repo-root commands/ folder is being ignored. This is cosmetic — nothing is broken (all Claude Code slash commands load fine), but it may confuse installers, so filing as an FYI + a question about whether it can be cleanly removed.

The warning

❯ agent-skills (user)
   Default commands/ folder is ignored because the manifest sets "commands"
   Remove "commands" from .claude-plugin/plugin.json (or SKILL.md
   frontmatter) to auto-load the folder, or add the folder's files to the
   "commands" list if you want both

Root cause

The repo serves multiple platforms, and two command directories sit side by side:

Location	Platform	Format
.claude/commands/*.md	Claude Code (manifest "commands": "./.claude/commands")	.md
.gemini/commands/*.toml	Gemini CLI	.toml
root commands/*.toml	Antigravity CLI (per README.md L310)	.toml

Claude Code's plugin loader auto-scans a root commands/ folder by default. Because .claude-plugin/plugin.json explicitly sets "commands": "./.claude/commands", the loader correctly uses that path and ignores the root commands/ folder — but emits the warning above about the collision.

Impact: none

• All Claude Code commands load correctly from .claude/commands/.
• The root commands/ folder is intentional — it's the Antigravity CLI command set and must stay. This is not a request to delete it.

So the warning is essentially Claude Code's loader being noisy about an intentional multi-platform layout.

Question / possible options (maintainer's call)

1. Does the Antigravity CLI plugin manifest (root plugin.json) support a configurable commands path? If so, relocating Antigravity's commands out of the repo root (e.g. into a dedicated subdir) would stop Claude Code's default root scan from colliding with the manifest override, and the warning would disappear for Claude Code users — without affecting Antigravity.
2. If Antigravity requires commands/ at the repo root (hardcoded convention), then this is likely just cosmetic / won't-fix. A short note in the Claude Code setup docs ("Claude Code may warn that the root commands/ folder is ignored — this is expected; it belongs to the Antigravity CLI") would save installers a moment of confusion.

Environment

• Installed via Claude Code plugin marketplace (addy-agent-skills), latest as of 2026-06-18.
• Manifest: .claude-plugin/plugin.json → "commands": "./.claude/commands".