docs(skills): collapse three overlapping skills trees into one verified tree

Three parallel trees documented the same ecosystem: omp-docs/skills/
(two overview pages), tools/npx-skills/ (10 pi-era npm pages), and
tools/vercel-labs-skills/ (11 CLI pages), plus a fourth leaderboard page
at engineering/skills-ecosystem.md. Verbatim overlap (identical SKILL.md
field tables in skills-spec.md vs skill-format.md; 13-agent vs 68-agent
copies of the same upstream table). Consolidated to four concept pages:

- skills/agent-skills.md: standard, format, loading, authoring (merges
  skills-spec, skill-format, skill-file-structure, skill-loading,
  best-practices, skills-vs-extensions)
- skills/skills-cli.md: CLI reference (merges commands, source-formats,
  installation-scope, skill-discovery, lock-file, env-variables,
  agent-support, related-links)
- skills/store-wiring.md: moved, fleet ops, links retargeted
- skills/ecosystem.md: replaces skills-ecosystem.md; stale 2026-08-12
  top-50 table dropped, replaced with a live top-10 re-queried from the
  skills.sh API tonight and the API contract re-verified (zero-based,
  200/page, {skills,total,hasMore,page}, total 9909)

All facts re-verified 2026-10-19 against primary sources:
agentskills.io, vercel-labs/skills README + src/cli.ts (command set,
--full-depth) + src/skill-lock.ts (v3 lock, XDG path, wipe-on-old),
live skills.sh API. Deleted superseded core/index-doc.md (old pi-era
docs index). Retargeted all inbound links (tools/index, engineering x3,
packages x3, pi/skills, core/index). Pi-era npm skill packaging is
listed as archived under /pi/.

Refs #29

omp-docs/tools/index.md

@@ -10,17 +10,17 @@ Configuration guides and reference material for installed software. Each tool ha
 * [comfyui](comfyui/index.md) — Node-based AI image generation engine on dankclaw. FLUX.2 klein 4B, CPU backend, systemd managed.
 * [live-sync](live-sync.md) — Heartbeat daemon committing machine-written paths (memories, managed-skills, live config, dotfiles) in the command-center checkout; systemd user timer, alerts via ntfy.
 * [[applications|applications]] — Default userspace applications on CachyOS with Niri — browsers, editor, terminal, file manager, audio, screenshots, gaming.
-* ](ghostty/index.md) — GPU-accelerated terminal emulator with extensive configuration, keybindings, and shaders.
-* ](gitea/index.md) — Private Git hosting on dankclaw. Quadlet-managed containers: Gitea, PostgreSQL, Caddy.
-* ](llama-cpp/index.md) — Local LLM inference server supporting GGUF models with OpenAI-compatible API.
+* [ghostty](ghostty/index.md) — GPU-accelerated terminal emulator with extensive configuration, keybindings, and shaders.
+* [gitea](gitea/index.md) — Private Git hosting on dankclaw. Quadlet-managed containers: Gitea, PostgreSQL, Caddy.
+* [llama.cpp](llama-cpp/index.md) — Local LLM inference server supporting GGUF models with OpenAI-compatible API.
 * [[linux-power-management|linux-power-management]] — Sleep/wake troubleshooting, NVIDIA GPU power management, and diagnostics for Linux systems.
 * [[noctalia-shell|noctalia-shell]] — Native desktop environment for Niri — launcher, control center, settings, lock screen, session menu, hotkey overlay, media controls, and system management.
 * [handy](handy.md) — Offline speech-to-text transcription with WebKitGTK backend and Tauri v2 UI.
 * [niri](niri/index.md) — Scrollable-tiling Wayland compositor — configuration, keybindings, and architecture for the workstation.
-* [npx Skills](npx-skills/index.md) — Distribution and installation tips for pi skill packages on npm, ecosystem overview, and skill specification.
+
 * [ornith-llama-cpp-setup](ornith-llama-cpp-setup/index.md) — Setup and reference for running Ornith MoE models with llama.cpp server for local inference.
 * [[tmux|tmux]] — Terminal multiplexer configuration, extended-keys setup, keyboard input best practices, and reload/restart procedures.
-* ](vercel-labs-skills/index.md) — Complete list of 68+ supported coding agents, their --agent flags, installation paths, and the SKILL.md specification.
+
 
 ## Adding a New Tool
 
@@ -28,16 +28,5 @@ Configuration guides and reference material for installed software. Each tool ha
 2. Add `index.md` as the entry point (no frontmatter for directory listings)
 3. Create concept files with frontmatter if content exceeds one file
 4. Update this index
-5. Log the change in `log.md`
 
-* [Default Applications](applications.md) — Default userspace applications on CachyOS with Niri — browsers, editor, terminal, file manager, audio, screenshots, gaming.
-
-* [CachyOS](cachyos.md) — Arch-based rolling release with performance-optimized kernels, repositories, and gaming stack. Running on the workstation.
-
-* [Linux Power Management](linux-power-management.md) — Sleep/wake troubleshooting, NVIDIA GPU power management, and diagnostics for Linux systems.
-
-* [Noctalia Shell](noctalia-shell.md) — Native desktop environment for Niri — launcher, control center, settings, lock screen, session menu, hotkey overlay, media controls, and system management.
-
-* [Handy](handy.md) — Offline speech-to-text transcription with WebKitGTK backend and Tauri v2 UI.
-
-* [tmux](tmux.md) — Terminal multiplexer configuration, extended-keys setup, keyboard input best practices, and reload/restart procedures.
+Skills tooling lives in [/skills/](../skills/index.md), not in this directory.