GitHub Copilot CLI

Section 2

Configuring & Customizing Copilot CLI

Every lever you can pull — instructions, skills, hooks, agents, plugins, extensions, and more.

📋

Repository Instructions

Scope: Entire repo · Always loaded

Persistent, repo-wide guidance loaded at session start. Coding standards, conventions, build commands, preferred patterns. Applied to every prompt automatically. Docs ↗

.github/copilot-instructions.md

🎯

Path-based Instructions

Scope: Matching files · Contextual

File-pattern specific instructions with applyTo glob in YAML frontmatter. Target TypeScript files, test directories, API routes, etc. Combines with repo-wide instructions.

.github/instructions/**/*.instructions.md

🤖

Agent Instructions

Scope: Repo root / CWD · Primary

Multi-agent instruction files at repo root. Supports AGENTS.md, CLAUDE.md, and GEMINI.md. Root-level files are treated as primary instructions.

AGENTS.md · CLAUDE.md · GEMINI.md

🏠

Local / Personal Instructions

Scope: All projects · User-level

Personal preferences applied across all repos. Coding style, communication preferences, tool choices. Also supports COPILOT_CUSTOM_INSTRUCTIONS_DIRS env var.

~/.copilot/copilot-instructions.md

⚡

Skills

Scope: On-demand · Task-specific

Folders of instructions, scripts, and resources loaded when relevant. SKILL.md with YAML frontmatter (name + description). Invoke with /skill-name or auto-detected. Open standard (agentskills spec). Docs ↗

.github/skills/<name>/SKILL.md · ~/.copilot/skills/

🔌

MCP Servers

Scope: Session · Extensibility

Model Context Protocol servers provide external tools and data sources. GitHub MCP server is built-in. Add custom servers for DBs, APIs, calendars, ticketing systems. Manage with /mcp add. Docs ↗

~/.copilot/mcp-config.json · /mcp add

🪝

Agent Hooks

Scope: Repository · Lifecycle events

Execute custom shell commands at key points: sessionStart, sessionEnd, preToolUse, postToolUse, userPromptSubmitted, agentStop, subagentStop, errorOccurred. Approve/deny tools programmatically, add logging, security scanning. Docs ↗

.github/hooks/*.json

🧑‍💼

Custom Agents

Scope: Repo / User / Org · Specialist personas

Define specialized personas in Markdown with YAML frontmatter: role, allowed tools, MCP connections, infer: true for auto-delegation. React reviewer, docs writer, security auditor, etc.

.github/agents/ · ~/.copilot/agents/ · .github-private/agents/

👥

Built-in Subagents

Scope: System · Always available

Pre-built specialized agents the CLI auto-delegates to: explore (codebase analysis), task (commands/builds), general-purpose (complex tasks), code-review (change analysis), research (deep investigation).

Automatic · /fleet for parallel execution

📦

Plugins

Scope: Installable bundles · New!

Packages that deliver agents + skills + hooks + MCP configs in one install. plugin.json manifest. Install from repos or marketplaces. Update, list, uninstall via /plugin. Docs ↗

plugin.json · copilot plugin install ./my-plugin

🏪

Plugin Marketplace

Scope: Distribution · Registry

Registry of plugins in a Git repo. marketplace.json in .github/plugin/. Users add with /plugin marketplace add org/repo. Official marketplaces: github/copilot-plugins, github/awesome-copilot.

.github/plugin/marketplace.json

🧩

Extensions New

Scope: Session · Experimental

Ask Copilot to write custom tools and hooks for itself using the @github/copilot-sdk. Extend the CLI with your own capabilities beyond built-in features. Enable with /experimental on. Added in v1.0.3. Changelog ↗

/experimental on · @github/copilot-sdk

🔍

LSP Servers

Scope: Code intelligence · Per-language

Language Server Protocol for go-to-definition, hover info, diagnostics. Configure per language with command, args, and file extension mappings. Manage with /lsp.

~/.copilot/lsp-config.json · .github/lsp.json

🧠

Copilot Memory

Scope: Persistent · Automatic learning

Copilot builds persistent understanding of your repository by storing "memories" — coding conventions, patterns, and preferences deduced while working. Reduces repetitive context in prompts.

Automatic · Persistent across sessions

🧭 When to Use What?

Requirement	Best Option
Copilot should always follow our repo conventions	Custom Instructions
I want a repeatable workflow I can invoke on demand	Skills
I want guardrails, policy, or automation around tool use	Hooks
I need Copilot to use tools from an external service	MCP Servers
I want Copilot to operate as a specialist for certain tasks	Custom Agent
I want to add a package of functionality without manual config	Plugin
I want to share plugins with my team or publicly	Plugin Marketplace
I want rich code intelligence (go-to-def, diagnostics)	LSP Servers

Section 3

Quick Start & Usage Guide

Install, launch, and master — every command, shortcut, and workflow pattern.

Installation

macOS / Linux (script)

curl -fsSL https://gh.io/copilot-install | bash

Homebrew

brew install copilot-cli

Windows (WinGet)

winget install GitHub.Copilot

npm (cross-platform)

npm install -g @github/copilot

Modes (Shift+Tab to cycle)

Interactive

Default

Conversational — Copilot asks before each action. You review and approve tool use step by step.

Plan

Shift+Tab

Structured planning — Copilot analyzes your request, asks clarifying questions, builds a plan before writing code.

Autopilot

Shift+Tab ×2

Autonomous — Copilot continues working until the task is complete. Experimental feature.

Typical Demo Flow

Launch

copilot

→

Trust & Auth

/login

→

Init Repo

/init

→

Give Task

Prompt

→

Agent Works

Read → Edit → Run

→

Review

/diff

→

Ship It

/delegate · git push

Essential Shortcuts

Shortcut	Action
`@file`	Include file contents in context
`#issue`	Reference GitHub issues, PRs, discussions New
`!cmd`	Run shell command directly
`&prompt`	Delegate to coding agent
`Shift+Tab`	Cycle modes (interactive → plan → autopilot)
`Ctrl+S`	Run command while preserving input
`Ctrl+T`	Toggle reasoning display
`Ctrl+O`	Expand recent timeline
`Ctrl+E`	Expand all timeline items
`Ctrl+G`	Edit prompt in external editor
`Ctrl+L`	Clear screen
`Esc`	Cancel current operation
`↑ / ↓`	Navigate command history
`Ctrl+R`	Search command history (reverse incremental search) New
`Ctrl+Z`	Suspend/resume (Unix platforms) New
`Esc-Esc`	Rewind file changes to any previous snapshot New
`Tab`	Resume local & remote coding agent sessions New
`Ctrl+C`	Cancel operation (×2 to exit session) New
`Ctrl+D`	Exit interactive session (Unix-style) New
`Shift+Enter`	Insert line break in prompt (Kitty protocol terminals) New
`Ctrl+Enter`	Submit multiline prompt New
`Page Up / Down`	Scroll in alt-screen mode; navigate in diff viewer New
`Ctrl+F / Ctrl+B`	Page down/up in scrollable views New
`Home / End`	Jump to top/bottom of scroll buffer; navigate in diff viewer New
`Ctrl+A`	Move cursor to beginning of line New
`Ctrl+K`	Delete from cursor to end of line New
`Ctrl+U`	Delete from cursor to beginning of line New
`Ctrl+W`	Delete word before cursor New
`Ctrl+H`	Delete character before cursor New
`Alt+← / →`	Move cursor by word New

Key Slash Commands

Command	Purpose
`/init`	Initialize copilot instructions for the repo
`/model`	Select AI model (Sonnet 4.6, Sonnet 4.5, GPT-5.4, etc.)
`/plan`	Create implementation plan before coding
`/review`	Run code review agent on changes
`/delegate`	Push work to Copilot coding agent (cloud)
`/fleet`	Parallel subagent execution
`/research`	Deep research with web + GitHub sources
`/diff`	Review all changes in current directory
`/undo`	Undo the last turn and revert file changes New
`/rewind`	Timeline picker to roll back to any point in conversation history New
`/pr`	Create PRs, fix CI failures, address review feedback, resolve conflicts New
`/compact`	Compress context to free token space
`/agent`	Browse and select custom agents
`/skills`	List, enable, disable, add, remove skills
`/mcp`	Add, edit, enable, disable, reload, auth MCP servers New
`/extensions`	View, enable, and disable CLI extensions New
`/restart`	Hot restart CLI while preserving session New
`/update`	View changelog and update instructions New
`/version`	Display CLI version and check for updates New
`/plugin`	Install, update, list, uninstall plugins
`/resume`	Resume a previous session
`/share`	Export session to file, GitHub gist, or HTML New
`/copy`	Copy the last response to clipboard New
`/context`	Show token usage visualization
`/usage`	Session metrics and statistics
`/chronicle`	Show session timeline and command history New
`/tasks`	View and manage background tasks New
`/changelog`	View recent release notes and updates New
`/ide`	Connect to an IDE workspace
`/lsp`	Manage language server configuration
`/clear`	Clear session history and context New
`/cwd`	Show or change working directory New
`/add-dir`	Add directory for file access New
`/list-dirs`	Show allowed directories New
`/session`	Display current session info New
`/theme`	Configure terminal theme (auto/dark/light) New
`/terminal-setup`	Enable multiline input mode New
`/reset-allowed-tools`	Reset all tool permissions New
`/user`	Show, list, or switch GitHub accounts New
`/login` / `/logout`	Sign in or out of Copilot New
`/exit` / `/quit`	Exit the CLI session ('exit' or 'quit' as bare commands also work) New
`/help`	Show all available commands and shortcuts New
`/feedback`	Submit feedback to GitHub New

CLI Flags (Command Line)

Flag	Purpose
`-p "prompt"`	Programmatic mode — execute and exit
`--autopilot`	Enable autonomous continuation
`--yolo`	Allow all permissions (alias: --allow-all)
`--model MODEL`	Select AI model
`--agent AGENT`	Use a specific custom agent
`--continue`	Resume most recent session
`--resume [ID]`	Resume a specific session
`--allow-tool 'X'`	Pre-approve specific tools
`--deny-tool 'X'`	Block specific tools
`--experimental`	Enable experimental features
`--acp`	Start Agent Client Protocol server
`-s / --silent`	Output only agent response (scripting)
`--max-autopilot-continues N`	Cap autopilot continuations
`--no-custom-instructions`	Skip loading instruction files
`--share [PATH]`	Export session transcript to markdown file New
`--share-gist`	Export session to shareable GitHub gist New
`--available-tools`	Allowlist specific tools for the session New
`--excluded-tools`	Denylist specific tools for the session New
`--additional-mcp-config`	Add MCP config files per-session New
`--output-format json`	Emit JSONL in prompt mode for programmatic integrations New
`--plugin-dir PATH`	Load a plugin from a local directory New
`--binary-version`	Query CLI binary version without launching New
`--mouse / --no-mouse`	Enable/disable mouse mode in alt screen New
`--bash-env`	Source BASH_ENV in shell sessions New
`--alt-screen on/off`	Control alternate screen buffer mode New

Deprecated Commands

Command	Status
`gh copilot suggest` / `gh cs`	Removed Oct 2025 — replaced by Copilot CLI interactive mode Deprecated
`gh copilot explain` / `gh ce`	Removed Oct 2025 — replaced by Copilot CLI interactive mode Deprecated
`gh-copilot` extension	Fully deprecated Oct 25, 2025 — migrate to standalone Copilot CLI Deprecated

Programmatic Examples

# Quick one-shot task
copilot -p "Add error handling to src/api.ts" --yolo

# Autonomous with limits
copilot --autopilot --yolo --max-autopilot-continues 10 \
  -p "Fix all failing tests"

# Specific permissions
copilot --allow-all-tools --deny-tool 'shell(rm)' \
  --deny-tool 'shell(git push)'

# Use a custom agent
copilot --agent=security-auditor -p "Audit this codebase"

# Resume last session
copilot --continue

# Pipe options from a script
./my-options.sh | copilot
            

Repository Configuration Structure

# Your repository
my-project/
├── .github/
│   ├── copilot-instructions.md         # Repo-wide instructions
│   ├── instructions/
│   │   ├── typescript.instructions.md  # Path-based (applyTo: "**/*.ts")
│   │   └── tests.instructions.md       # Path-based (applyTo: "**/*.test.*")
│   ├── skills/
│   │   └── deploy/
│   │       └── SKILL.md                # Skill definition
│   ├── agents/
│   │   └── reviewer.agent.md           # Custom agent
│   ├── hooks/
│   │   └── security.json               # Hook configuration
│   ├── plugin/
│   │   └── marketplace.json            # Plugin marketplace
│   └── lsp.json                        # LSP server config
├── AGENTS.md                           # Agent instructions
└── ...

# Your home directory
~/.copilot/
├── copilot-instructions.md             # Personal instructions
├── mcp-config.json                     # MCP server config
├── lsp-config.json                     # LSP config (user-level)
├── config.json                         # CLI settings
├── skills/                             # Personal skills
└── agents/                             # Personal agents
            

The GitHub Copilot Ecosystem

Configuring & Customizing Copilot CLI

🧭 When to Use What?

Quick Start & Usage Guide