fix: restore SKILL.md citation metadata and remove superseded skills/ directory

[Copilot]

The auto-regeneration workflow was overwriting SKILL.md without a citation field, stripping attribution metadata on every run. Additionally, the skills/ directory (individual *_skill.md files plus index.json and bizard_skills.json) was no longer needed after the unified SKILL.md approach was adopted.

Changes

• SKILL.md — Restored citation field in YAML frontmatter:

  metadata:
      skill-author: Bizard Collaboration Group, Luo Lab, and Wang Lab
      website: https://openbiox.github.io/Bizard/
      repository: https://github.com/openbiox/Bizard
      citation: >
        - Li, K., Zheng, H., ... & Wang, S. (2026). Bizard: A Community‐Driven Platform
          for Accelerating and Enhancing Biomedical Data Visualization. iMetaMed, e70038.
          https://doi.org/10.1002/imm3.70038

• generate_skills.py — generate_unified_skill() now accepts the in-memory skills list directly and writes SKILL.md without producing any JSON or per-tutorial markdown output. The citation field is included in every regeneration. Removed the now-unused skill_file key from all returned skill dicts.

• generate-skills.yml — Simplified to only generate and commit SKILL.md. Removed incremental file processing, --format/--output arguments, and all skills/ directory references.

• skill-command.yml — Removed the files dispatch input; the /skill command now always regenerates all tutorials.

• skills/ — Entire directory removed: all 259 individual *_skill.md files, skills/index.json, and skills/bizard_skills.json.

• Skills.qmd / Skills.zh.qmd — Systematic update: removed the interactive skills browser widget (which fetched skills/index.json), removed JSON file download links, removed the redundant "Download Resources" section, updated all skill.md references to SKILL.md (including #file:SKILL.md hint and Quick start callout), and updated regeneration instructions.

• skill-spec.md — Updated "File Naming" section to describe the unified SKILL.md output instead of individual per-tutorial files; removed the "JSON Index Format" section (skills/index.json and skills/bizard_skills.json); added a "Regenerating SKILL.md" section.

• quarto-publish.yml — Removed the stale - 'skills/**' entry from paths-ignore.

• .gitignore — Added skills/ to ignore the entire directory.

[github-actions]

✅ QMD Format Check

No new QMD tutorial files to check.

Automated check by the PR Review workflow.
See contribution guidance for the expected tutorial format.

[ShixiangWang]

@copilot 整个 skill 目录是不是可以都删除了 包括文件 https://github.com/openbiox/Bizard/blob/main/skills/index.json 和 https://github.com/openbiox/Bizard/blob/main/skills/bizard_skills.json， action也完全没必要更新这一块了。

[Copilot]

@copilot 整个 skill 目录是不是可以都删除了 包括文件 https://github.com/openbiox/Bizard/blob/main/skills/index.json 和 https://github.com/openbiox/Bizard/blob/main/skills/bizard_skill...

Done in cd7c325. The entire skills/ directory has been removed (including index.json and bizard_skills.json). The skill generation workflow is also simplified:

• generate_skills.py now builds SKILL.md directly from the in-memory skills list — no JSON output, no skills/ directory needed
• generate-skills.yml only generates and commits SKILL.md
• Skills.qmd / Skills.zh.qmd: removed the skills browser widget (which fetched skills/index.json) and the JSON file download links
• .gitignore now ignores the entire skills/ directory

[ShixiangWang]

@copilot

https://github.com/openbiox/Bizard/blob/main/Skills.qmd 和 https://github.com/openbiox/Bizard/blob/main/Skills.zh.qmd 也需要系统更新。检查仓库其他相关文件是不是也需要系统更新。

[Copilot]

@copilot

https://github.com/openbiox/Bizard/blob/main/Skills.qmd 和 https://github.com/openbiox/Bizard/blob/main/Skills.zh.qmd 也需要系统更新。检查仓库其他相关文件是不是也��...

Done in b924ff4. Here's a summary of all files updated:

• Skills.qmd / Skills.zh.qmd: Removed the redundant "Download Resources" section (leftover from previous edit), removed the skills browser widget (was fetching skills/index.json), updated all skill.md → SKILL.md references (including #file:SKILL.md Copilot Chat hint and the Quick start callout)
• skill-spec.md: Replaced the "File Naming" (skills/<Category>/...) section with an "Output: Unified SKILL.md" section; removed the "JSON Index Format" section (skills/index.json and skills/bizard_skills.json); added a "Regenerating SKILL.md" section
• generate_skills.py: Removed the now-unused skill_file key from both skill dict return paths (offline and LLM mode)
• quarto-publish.yml: Removed the stale - 'skills/**' entry from paths-ignore (the directory no longer exists)