Fix context initialization by using AGENTS.md instead of AGENT.md

scientific-helpers/scientific-context-initialization/references/AGENTS.md

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+# Reference: Complete Context Initialization Template
+
+This is the complete reference template for what gets added to the workspace root `AGENTS.md` file.
+
+---
+
+# Agent Scientific Skills - Working Instructions
+
+## IMPORTANT: Use Available Skills First
+
+Before attempting any scientific task, use available skills.
+
+---
+
+## Database Access Tasks
+
+**Before writing any database access code, use available skills in this repository.**
+
+This repository contains skills for 24+ scientific databases. Each skill includes:
+- API endpoints and authentication patterns
+- Working code examples
+- Best practices and rate limits
+- Example scripts
+
+Always use available database skills before writing custom database access code.
+
+---
+
+## Scientific Package Usage
+
+**Before writing analysis code with scientific packages, use available skills in this repository.**
+
+This repository contains skills for 40+ scientific Python packages. Each skill includes:
+- Installation instructions
+- Complete API usage examples
+- Best practices and common patterns
+- Working scripts and reference documentation
+
+Always use available package skills before writing custom analysis code.
+
+---
+
+## Laboratory Platform Integration
+
+**Before writing any platform integration code, use available skills in this repository.**
+
+This repository contains skills for 6+ laboratory platforms and cloud services. Each skill includes:
+- Authentication and setup instructions
+- API access patterns
+- Working integration examples
+- Platform-specific best practices
+
+Always use available integration skills before writing custom platform code.
+
+---
+
+## Scientific Analysis & Research Methods
+
+**Before attempting any analysis, writing, or research task, use available methodology skills in this repository.**
+
+This repository contains skills for scientific methodologies including:
+- Data analysis frameworks (EDA, statistical analysis)
+- Research methodologies (hypothesis generation, brainstorming, critical thinking)
+- Communication skills (scientific writing, visualization, peer review)
+- Document processing (DOCX, PDF, PPTX, XLSX)
+
+Always use available methodology skills before attempting scientific analysis or writing tasks.
+
+---
+
+*This file is auto-generated by context-initialization skills. It ensures the agent uses available skills before attempting to solve scientific tasks from scratch.*
+
+