Understanding AI Coding Agents
A comprehensive guide to AI coding assistants, skills, rules, and how they work together to supercharge your research workflow.
What Are AI Coding Agents?
AI coding agents are intelligent assistants that can read, understand, and write code. Unlike simple autocomplete tools, these agents can:
- Understand context — Read your entire project structure, documentation, and existing code
- Execute tasks autonomously — Run commands, create files, and make changes across multiple files
- Follow instructions — Adhere to project-specific conventions and coding standards
- Learn from feedback — Improve based on corrections and preferences you provide
Popular AI Coding Agents
Example: Using an AI Agent for Economics Research
$ claude
> Analyze this panel dataset using a difference-in-differences
approach with state and year fixed effects. Use robust
standard errors clustered at the state level.
✓ Reading data from treatment_data.dta
✓ Generating Stata code with reghdfe
✓ Adding clustered standard errors
✓ Creating event study plot
✓ Exporting results to LaTeX table
What Are Skills?
Skills are reusable instruction sets that teach AI agents how to perform specific tasks. Think of them as "expert knowledge packages" that you can plug into your agent.
The Agent Skills standard defines a portable format using SKILL.md files that work across multiple AI tools.
Without Skills
You must explain every detail each time: "Use Stata's reghdfe package with clustered standard errors, format output as LaTeX, follow AER style guidelines..."
With Skills
Just say: "Run a DiD analysis on this data" — the skill handles all the domain-specific knowledge automatically.
Skill Structure (SKILL.md)
A skill is a folder containing a SKILL.md file with metadata and instructions:
# Folder structure
r-econometrics/
├── SKILL.md # Required: instructions + metadata
├── scripts/ # Optional: helper scripts
├── references/ # Optional: documentation
└── assets/ # Optional: templates, data
# Example SKILL.md
---
name: r-econometrics
description: Run econometric analyses in R using fixest, modelsummary
workflow_stage: analysis
compatibility:
- claude-code
- cursor
- gemini-cli
tags: [regression, panel-data, did]
---
# R Econometrics
## Purpose
Use this skill for econometric analysis in R, including
difference-in-differences, instrumental variables, and
regression discontinuity designs.
## Instructions
1. Use the fixest package for fixed effects estimation
2. Always report heteroskedasticity-robust standard errors
3. Create coefficient plots using ggplot2
4. Export tables in LaTeX format using modelsummary
How Skills Work: Progressive Disclosure
- Discovery — Agent loads only skill names and descriptions at startup
- Activation — When a task matches, the full instructions are loaded
- Execution — Agent follows instructions, using bundled scripts/assets as needed
What Are Rules?
Rules are project-level configuration files that provide persistent instructions to AI agents. They define coding standards, project conventions, and preferences that should apply to all interactions.
🔧 Project Rules
Live in your repository. Shared with all contributors. Version controlled.
AGENTS.md
👤 Personal Rules
Apply to all your projects. Your individual preferences.
~/.claude/CLAUDE.md
🏢 Team Rules
Organization-wide standards managed by IT/DevOps.
Managed policies
What to Include in Rules
- Build commands — How to install dependencies, run tests, build the project
- Code style — Formatting preferences, naming conventions, patterns to use
- Project structure — Where files should go, how modules are organized
- Domain knowledge — Project-specific terminology, data sources, methodologies
- Security rules — Files to never modify, secrets handling, compliance requirements
Example: Rules for an Economics Research Project
# AGENTS.md
## Project Overview
This repository contains replication files for our JEL submission
on minimum wage effects in developing countries.
## Data
- Raw data is in `data/raw/` — NEVER modify these files
- Processed data goes in `data/processed/`
- All data cleaning must be reproducible via `make data`
## Code Style
- Stata: Use `reghdfe` for fixed effects, cluster at state level
- R: tidyverse style, use `fixest` for estimation
- All tables in LaTeX format following AER guidelines
## Testing
- Run `make test` before committing
- Ensure all figures reproduce exactly
AGENTS.md vs CLAUDE.md
Both are rule files, but they serve different purposes and have different scopes:
| Aspect | AGENTS.md | CLAUDE.md |
|---|---|---|
| Scope | Project-specific | Personal (all projects) |
| Location | Repository root | ~/.claude/CLAUDE.md |
| Version Control | ✓ Committed to git | ✗ Local only |
| Shared With Team | ✓ Yes | ✗ No |
| Compatibility | 60k+ projects, many agents | Claude Code only |
| Best For | Build commands, project structure, team conventions | Personal preferences, communication style |
💡 Pro Tip: Use Both
Put project-specific instructions (build commands, data handling) in AGENTS.md so your collaborators benefit too. Keep personal preferences (response style, your favorite packages) in CLAUDE.md.
Other Tool-Specific Files
Different tools may have their own configuration files that work alongside AGENTS.md:
.cursorrules— Cursor-specific rules (being unified with AGENTS.md).gemini/settings.json— Gemini CLI configuration.github/copilot-instructions.md— GitHub Copilot instructions
Skills vs Subagents
These terms are sometimes confused, but they serve fundamentally different purposes:
🛠️ Skills
What: Instruction sets (text files) that teach an agent HOW to do something
Analogy: A recipe book — provides knowledge and procedures
When loaded: On-demand when relevant to the task
Execution: Main agent follows the instructions
🤖 Subagents
What: Separate AI instances spawned to handle specific subtasks
Analogy: Hiring a contractor — delegates work to another worker
When spawned: For parallelizable or isolated tasks
Execution: Independent agent runs, returns results
Example: When to Use Each
"Run a DiD analysis following best practices"
→ The agent needs domain knowledge on HOW to do DiD correctly
"Search the codebase for all files that use this dataset"
→ An independent search task that can run in parallel
"Format this regression output as a LaTeX table"
→ Needs knowledge of formatting conventions
"Read all 50 do-files and summarize what variables each creates"
→ Large, parallelizable reading task
Key Differences
| Skills | Subagents | |
| Purpose | Add knowledge | Parallelize work |
| Context | Shares main context | Isolated context |
| Can edit files | ✓ (via main agent) | Usually read-only |
| Persistent | ✓ Reusable files | ✗ Ephemeral |
How They Work Together
All these components form a hierarchy that guides how AI agents understand and work on your project:
Company-wide standards, security requirements
Your personal preferences across all projects
Project rules, conventions, build commands
Domain expertise loaded on-demand
Specific instructions for this task (highest priority)
Resolution Order
When instructions conflict, more specific ones win:
Your prompt > Nearest AGENTS.md > Project root AGENTS.md > User CLAUDE.md > Org policies
Real-World Example: Economics Research Workflow
Agent reads AGENTS.md: learns about your data structure, Stata conventions, and that raw data must never be modified.
Agent activates the stata-econometrics skill: now knows to use reghdfe, cluster standard errors, and format output for AER.
Your prompt overrides the skill's default of OLS — agent adapts while keeping all other conventions.
Parallel search through your do-files to check for consistency with existing analyses.
Resources & Documentation
🛠️ Agent Skills Standard
Official specification for SKILL.md format
agentskills.io →📄 AGENTS.md
Open format for guiding coding agents
agents.md →🤖 Claude Code Docs
Official documentation for Claude Code
docs.anthropic.com →⌨️ Cursor Documentation
Learn about Cursor's AI features and rules
cursor.com/docs →✨ Gemini CLI
Google's AI-powered command-line tool
github.com →🐙 OpenAI Codex
OpenAI's coding agent documentation
openai.com →Ready to Get Started?
Browse our curated collection of economics-specific AI skills.