Gemini CLI vs Junie | agentconfig.ing

Gemini CLI vs JunieComparisonUpdated 2026-03-16

SUMMARY

Gemini CLI (CLI) uses markdown configuration while Junie (Agent) uses markdown. They differ on 3 of 11 compared features. Both tools provide AI-assisted development but take different approaches to project configuration.

FEATURE COMPARISON

Feature	Gemini CLI	Junie	Notes
Config format	markdown	markdown
Hierarchy support	✓	✗	Whether config files can be placed at multiple directory levels
Global config	✓	✗	User-wide configuration outside any project
Project config	✓	✓
Subdirectory scoping	✗	✗	Config files in subdirectories that apply only to that subtree
File inclusion / imports	✗	✗	Ability to include or reference other files from config
Ignore file	✗	✗
IDE integration	CLI	Agent
Schema / structure	Free-form (Markdown)	Free-form (Markdown)	Whether config uses structured schema or free-form content
Git committed	✓	✓	Whether primary config files are intended to be version-controlled
Encoding	UTF-8	UTF-8

FILE MAPPING

Purpose	Gemini CLI	Junie
Project instructions	GEMINI.md	.junie/guidelines.md
Project instructions	.gemini/styleguide.md	AGENTS.md

SIDE-BY-SIDE CODE SAMPLES

Gemini CLI

GEMINI.md

markdown

# Project Context

## Stack
- Node.js 22 with TypeScript 5.x
- Express.js for the API server
- Prisma ORM with PostgreSQL
- React 19 with Vite for the frontend

## Architecture
- Monorepo with pnpm workspaces
- packages/api — Express REST API
- packages/web — React SPA
- packages/shared — Shared types and utilities

## Commands
- pnpm dev — Start all services
- pnpm test — Run vitest across all packages
- pnpm lint — ESLint + Prettier check
- pnpm db:migrate — Run Prisma migrations

## Conventions
- Use barrel exports (index.ts) for public APIs
- Error responses use RFC 7807 Problem Details format
- All API endpoints require authentication except /health

Junie

.junie/guidelines.md

markdown

# Project Guidelines

## Language & Framework
- Kotlin with Spring Boot 3.x
- Gradle with Kotlin DSL
- JDK 21 with virtual threads

## Architecture
- Hexagonal architecture (ports & adapters)
- Domain events for cross-module communication
- CQRS for read-heavy endpoints

## Code Standards
- Follow Kotlin coding conventions
- Use data classes for DTOs
- Prefer sealed classes for domain errors
- Extension functions over utility classes

## Testing
- JUnit 5 with Kotest assertions
- Testcontainers for integration tests
- MockK for mocking (not Mockito)

## Build & Run
- Build: ./gradlew build
- Test: ./gradlew test
- Run: ./gradlew bootRun

KEY DIFFERENCES

1. Hierarchy support

Gemini CLI: Supported. Junie: Not supported.

2. Global config

Gemini CLI: Supported. Junie: Not supported.

3. IDE integration

Gemini CLI: CLI. Junie: Agent.

WHICH SHOULD I USE?

Recommendation

Choose based on your IDE/CLI preference. If you use Gemini CLI, configure GEMINI.md. If you use Junie, configure .junie/guidelines.md. Many projects include config files for multiple tools so each team member can use their preferred editor.

PORTABILITY TIP

sync-instructions.sh

bash

# Maintain a single source of truth:
cp AI-INSTRUCTIONS.md CLAUDE.md
cp AI-INSTRUCTIONS.md .cursorrules
cp AI-INSTRUCTIONS.md AGENTS.md