Adapt all skills for GPT Codex-compatible execution

README.md

@@ -1,9 +1,18 @@
 # Research Skills
 
-A collection of Claude Code skills for academic research workflows.
+A collection of research workflow skills for Claude Code and GPT Codex.
 
 ## Skills
 
+
+## Platform Compatibility
+
+These skills now support **Claude Code and GPT Codex** with the same core workflow.
+
+- Keep the workflow, structure, and outputs unchanged.
+- Map tool calls by capability (e.g., literature search, PDF parsing, reference retrieval) instead of provider-specific names.
+- When a platform-specific tool is unavailable, use fallback commands/APIs documented in each skill.
+
 | Skill | Description | Trigger |
 |-------|-------------|---------|
 | [medical-imaging-review](./medical-imaging-review/) | Write comprehensive literature reviews for medical imaging AI | `/medical-imaging-review`, "review paper", "survey", "综述" |
@@ -12,7 +21,7 @@ A collection of Claude Code skills for academic research workflows.
 
 ## Installation
 
-Copy the desired skill folder to your Claude Code skills directory:
+Copy the desired skill folder to your skills directory (Claude Code or Codex-compatible runtime):
 
 ```bash
 # For medical-imaging-review

medical-imaging-review/SKILL.md

@@ -45,6 +45,21 @@ Write comprehensive literature reviews following a systematic 7-phase workflow.
 
 ---
 
+
+## Codex Compatibility Mode
+
+This skill can run in GPT Codex with the same 7-phase workflow.
+
+### Tool Mapping (capability-first)
+- ArXiv search/read: use any available arXiv MCP, REST API, or browser search pipeline.
+- PubMed search: use PubMed MCP when available; otherwise use E-utilities/WebSearch fallback.
+- Zotero retrieval: use Zotero MCP first; fallback to local Zotero Web API endpoints.
+
+### Execution Fallback
+If a listed tool is unavailable in the current runtime, continue with equivalent tooling and keep output schema unchanged (`CLAUDE.md`, `IMPLEMENTATION_PLAN.md`, `manuscript_draft.md`).
+
+---
+
 ## Core Principles
 
 ### Writing Style

paper-slide-deck/SKILL.md

@@ -9,6 +9,21 @@ Transform academic papers and content into professional slide deck images with a
 
 ## Usage
 
+
+## Codex Compatibility Mode
+
+This skill can run in GPT Codex without changing the slide workflow.
+
+### Interaction Mapping
+- `AskUserQuestion` steps become standard conversational confirmations in Codex.
+- Script execution remains identical (`scripts/`), run with local shell tooling.
+- Gemini API path remains optional; if unavailable, stop at outline-only mode or use extracted paper figures only.
+
+### Runtime Rule
+Prefer deterministic local scripts first (`detect-figures.ts`, `extract-figure.ts`, `merge-to-pptx.ts`, `merge-to-pdf.ts`), then optional external generation APIs.
+
+---
+
 ```bash
 /paper-slide-deck path/to/paper.pdf
 /paper-slide-deck path/to/paper.pdf --style academic-paper
@@ -223,7 +238,7 @@ Multiple sources supported: text, images, files from conversation.
 
 ### Step 3: User Confirmation
 
-**Single AskUserQuestion with all applicable options:**
+**Single user confirmation checkpoint with all applicable options (use normal chat or `AskUserQuestion`):**
 
 | Question | When to Ask |
 |----------|-------------|
@@ -251,7 +266,7 @@ If `--outline-only`, stop here.
 
 **Before generating images**, ask user to choose generation method:
 
-**Use AskUserQuestion** with options:
+**Ask the user to choose** with options (normal chat or `AskUserQuestion`):
 
 | Option | Label | Description |
 |--------|-------|-------------|

research-proposal/SKILL.md

@@ -32,6 +32,21 @@ allowed-tools:
 
 # Research Proposal Generator
 
+
+## Codex Compatibility Mode
+
+This workflow is fully portable to GPT Codex. Keep the same 5 phases and output format.
+
+### Interaction Mapping
+- `AskUserQuestion` → normal conversational checkpoint in Codex (explicit numbered questions).
+- Zotero MCP calls → any available Zotero connector with equivalent fields.
+- WebSearch/arXiv/PubMed steps remain unchanged by intent; only tool names may differ.
+
+### Portability Rule
+When an exact tool is missing, preserve the phase objective and substitute equivalent retrieval/generation commands.
+
+---
+
 Generate high-quality academic research proposals for PhD applications following Nature Reviews-style academic writing conventions.
 
 ## Overview
@@ -50,7 +65,7 @@ This skill guides the generation of research proposals through a structured 5-ph
 
 ## Phase 1: Requirements Gathering
 
-Use `AskUserQuestion` to collect the following information:
+Use an explicit user Q&A checkpoint (or `AskUserQuestion` if available) to collect the following information:
 
 ### Required Information
 
@@ -236,7 +251,7 @@ Read the reference file for domain-specific guidance:
 
 ### User Confirmation
 
-**CRITICAL**: Present the outline to the user and wait for confirmation before proceeding to content generation.
+**CRITICAL**: Present the outline to the user and wait for explicit confirmation before proceeding to content generation (via normal chat or `AskUserQuestion`).
 
 ```
 Present the generated outline and ask: