Code-tab Customize -> Skills is missing skills that are present in ~/.claude/skills (non-deterministic; / menu and engine load them all)

[privacyguy123]

Preflight Checklist

• I have searched existing issues and this hasn't been reported yet
• This is a single bug report
• I am using a recent build (Claude Desktop 1.9659.2 / engine 2.1.156)

Summary

In the Code tab, Customize → Skills → Personal skills shows only a small, non-deterministic subset of the skills that are actually present in ~/.claude/skills/. Most skills in that folder are missing from the panel, even though the Claude Code engine loads them all — they appear and work in the / slash menu. Which skills the panel shows even changes between opens.

Environment

• Claude Desktop (Windows): 1.9659.2 (x64 / MSIX)
• Bundled Claude Code engine: 2.1.156
• OS: Windows 10 Pro 19045

Repro

1. Have several skills in ~/.claude/skills/ (each a folder containing SKILL.md).
2. Open the Code tab → Customize → Skills.
3. Observe that Personal skills lists only ~2 entries, while the folder contains many more.
4. Open the / slash menu in a session — all of the skills are present and usable.
5. Re-open Customize → Skills — the ~2 shown may be a different pair.

Observed on my machine

• ~/.claude/skills/ contains 19 skill folders.
• The / slash menu and the engine load all 19 (plus plugin skills) correctly.
• Customize → Personal skills shows only ~2, and which 2 is not stable across opens (e.g. find-skills+idapython on one open, idapython+skill-creator on another).
• The omission is independent of whether the skill folder is a real directory or a symlink. Of my 19 folders, 17 are symlinks (installed via npx skills, pointing into ~/.agents/skills/) and 2 are real directories (playwright-cli, screenshot). Both real-directory skills are missing from the panel, while some symlinked skills are shown — so symlinking is not the determinant.

Expected

Customize → Skills should deterministically list every skill the engine loads from ~/.claude/skills/, matching what appears in the / slash menu.

Notes

• Not frontmatter-shape related: skills with only name/description and skills with extra keys (allowed-tools, license, metadata, …) are both affected, and the desktop's skill schema strips unknown keys rather than rejecting them.
• The / slash menu and the engine are the source of truth and are unaffected — this is specific to the Customize panel's skill enumeration/rendering.
• Context (not the cause): many of these skills were installed via npx skills, which symlinks ~/.claude/skills/<name> → ~/.agents/skills/<name>. The symlink detail is incidental given that real-directory skills are dropped too.

[sum117]

Same install layout here on Windows 11: npx skills links each skill into ~/.claude/skills as a junction into ~/.agents/skills, plus a couple of real-directory skills. The engine loaded all of them (they showed in the model's skill list).

I had filed #68318 blaming the junctions specifically, since a junction reports isDirectory() as false in Node and Bun readdir. Your determinant rules that out: your real-directory skills are dropped too and it is non-deterministic. I have closed mine as a duplicate of this. Thanks for the precise repro.

[dmarreco]

Also seeing this for project-level skills (.claude/skills/ at the repo root, not just ~/.claude/skills/), so it's not limited to the personal/user scope.

Repo: workspace with .claude/skills//SKILL.md (8 skills: confluence-reader, confluence-writer, gitlab-reader, grafana-log-reader, grill-me, jira-reader, sonar-reader, write-a-skill), each with valid frontmatter (name, description).
What works: all 8 show up in the / slash menu and are listed in the engine's available-skills system-reminder; invoking any of them (e.g. /gitlab-reader) works correctly.
What's broken: none of these appear in Customize → Skills in the settings UI.
Platform: macOS, Claude Code CLI 2.1.195.
Same pattern as the original report — engine/slash-menu enumeration is correct, Customize panel enumeration is not — just confirming it spans both user and project skill scopes.