Agent Customization

Decision Flow

Primitive When to Use

Workspace Instructions Always-on, applies everywhere in the project

File Instructions Explicit via applyTo patterns, or on-demand via description

MCP Integrates external systems, APIs, or data

Hooks Deterministic shell commands at agent lifecycle points (block tools, auto-format, inject context)

Custom Agents Subagents for context isolation, or multi-stage workflows with tool restrictions

Prompts Single focused task with parameterized inputs

Skills On-demand workflow with bundled assets (scripts/templates)

Quick Reference

Consult the reference docs for templates, domain examples, advanced frontmatter options, asset organization, anti-patterns, and creation checklists. If the references are not enough, load the official documentation links for each primitive.

Type File Location Reference

Workspace Instructions copilot-instructions.md , AGENTS.md

.github/ or root Link

File Instructions *.instructions.md

.github/instructions/

Link

Prompts *.prompt.md

.github/prompts/

Link

Hooks *.json

.github/hooks/

Link

Custom Agents *.agent.md

.github/agents/

Link

Skills SKILL.md

.github/skills/<name>/ , .agents/skills/<name>/ , .claude/skills/<name>/

Link

User-level: {{USER_PROMPTS_FOLDER}}/ (*.prompt.md, *.instructions.md, *.agent.md; not skills) Customizations roam with user's settings sync

Creation Process

If you need to explore or validate patterns in the codebase, use a read-only subagent. If the ask-questions tool is available, use it to interview the user and clarify requirements.

Follow these steps when creating any customization file.

1. Determine Scope

Ask the user where they want the customization:

• Workspace: For project-specific, team-shared customizations → .github/ folder

• User profile: For personal, cross-workspace customizations → {{USER_PROMPTS_FOLDER}}/

2. Choose the Right Primitive

Use the Decision Flow above to select the appropriate file type based on the user's need.

3. Create the File

Create the file directly at the appropriate path:

• Use the location tables in each reference file

• Include required frontmatter as needed

• Add the body content following the templates

4. Validate

After creating:

• Confirm the file is in the correct location

• Verify frontmatter syntax (YAML between --- markers)

• Check that description is present and meaningful

Edge Cases

Instructions vs Skill? Does this apply to most work, or specific tasks? Most → Instructions. Specific → Skill.

Skill vs Prompt? Both appear as slash commands in chat (type / ). Multi-step workflow with bundled assets → Skill. Single focused task with inputs → Prompt.

Skill vs Custom Agent? Same capabilities for all steps → Skill. Need context isolation (subagent returns single output) or different tool restrictions per stage → Custom Agent.

Hooks vs Instructions? Instructions guide agent behavior (non-deterministic). Hooks enforce behavior via shell commands at lifecycle events like PreToolUse or PostToolUse — they can block operations, require approval, or run formatters deterministically. See hooks reference.

Common Pitfalls

Description is the discovery surface. The description field is how the agent decides whether to load a skill, instruction, or agent. If trigger phrases aren't IN the description, the agent won't find it. Use the "Use when..." pattern with specific keywords.

YAML frontmatter silent failures. Unescaped colons in values, tabs instead of spaces, name that doesn't match folder name — all cause silent failures with no error message. Always quote descriptions that contain colons: description: "Use when: doing X" .

applyTo: "" burns context. This means "always included for every file request" — it loads the instruction into the context window on every interaction, even when irrelevant. Use specific globs (/*.py , src/api/** ) unless the instruction truly applies to all files.