Plugin skills from skills/ directory invisible in slash command autocomplete, blocking adoption

Description

Plugin skills loaded from the skills/<name>/SKILL.md directory structure do not appear in the / slash command autocomplete dropdown, while equivalent commands from the legacy commands/ directory do. This is blocking plugin authors from adopting the Agent Skills open standard (skills/ + SKILL.md).

Context: Why this matters now

I maintain cc-spex, a plugin built on top of spec-kit. When I followed suit and migrated from commands/ to skills/, all slash command autocompletion broke. Skills load correctly (the model sees them, they execute when fully typed), but users can't discover them via / autocomplete. I had to revert the migration to keep the plugin usable.

This creates an awkward situation: spec-kit generates skills/, Claude Code documents skills/ as the standard, but the UI doesn't support skills/ for autocomplete. Plugin authors are stuck maintaining commands/ as a workaround.

Steps to Reproduce

1. Create a plugin with skills in skills/<skill-name>/SKILL.md (no commands/ directory)
2. Install via marketplace (extraKnownMarketplaces with directory source)
3. Start Claude Code
4. Type / or /pluginname: in the prompt

Expected: Plugin skills appear in the autocomplete dropdown
Actual: Dropdown is empty for the plugin's namespace. No skills appear.

1. Type the full skill name (e.g., /pluginname:init) and press Enter

Result: Skill executes correctly, confirming it's loaded.

Environment

• Claude Code: v2.1.91 (CLI)
• OS: macOS Darwin 25.4.0
• Plugin structure: marketplace with "source": "./spex", skills in spex/skills/<name>/SKILL.md
• Plugin manifest: .claude-plugin/plugin.json (no explicit skills field, auto-detected)

Relation to existing issues

This is the same root issue as #18949 (Jan 2026), which remains open. Adding this as a concrete case with:

• Source code analysis pointing to where the disconnect likely is
• A real-world revert that demonstrates the impact on plugin adoption
• Context that the upstream tooling (spec-kit) has already moved to skills-only

Other related: #17271, #17509, #20935, #28555, #35641, #42038

Impact

This bug effectively blocks the ecosystem from migrating to the Agent Skills standard. Plugin authors who want their skills discoverable via autocomplete must maintain the legacy commands/ directory, which contradicts the documented direction.