Refactor prompt integration and add agent integration

.gitignore

@@ -60,6 +60,3 @@ docs/wip/
 .env.local
 .env.*.local
 AGENTS.md
-
-# APM dependencies
-apm_modules/

CHANGELOG.md

@@ -6,6 +6,19 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 
+## [0.5.4]
+
+### Added
+- **Agent Integration**: Automatic sync of `.agent.md` files to `.github/agents/` with `-apm` suffix (same pattern as prompt integration)
+
+### Fixed
+- `sync_integration` URL normalization bug that caused ALL integrated files to be removed during uninstall instead of only the uninstalled package's files
+  - Root cause: Metadata stored full URLs (`https://github.com/owner/repo`) while dependency list used short form (`owner/repo`)
+  - Impact: Uninstalling one package would incorrectly remove prompts/agents from ALL other packages
+  - Fix: Normalize both URL formats to `owner/repo` before comparison
+  - Added comprehensive test coverage for multi-package scenarios
+- Uninstall command now correctly removes only `apm_modules/owner/repo/` directory (not `apm_modules/owner/`)
+
 ## [0.5.3] - 2025-11-16
 
 ### Changed

README.md

@@ -15,8 +15,9 @@
 
 📦 **Mix and match what your team needs**:
 
-- **Agents** - Agentic workflows (.prompt.md files)
-- **Context** - Company rules, standards, knowledge (.instructions.md files) and domain boundaries (.chatmode.md)
+- **Agents** - AI personas (.agent.md files)
+- **Prompts** - Executable workflows (.prompt.md files)
+- **Context** - Company rules, standards, knowledge (.instructions.md files)
 
 ![APM Demo](docs/apm-demo.gif)
 

docs/getting-started.md

@@ -284,12 +284,14 @@ This creates a complete Context structure:
 my-first-project/
 ├── apm.yml              # Project configuration
 └── .apm/
-    ├── chatmodes/       # AI assistant personalities  
+    ├── agents/          # AI assistant personalities
     ├── instructions/    # Context and coding standards
     ├── prompts/         # Reusable agent workflows
     └── context/         # Project knowledge base
 ```
 
+> **Note**: Legacy `.apm/chatmodes/` directory with `.chatmode.md` files is still supported.
+
 ### 2. Explore Generated Files
 
 Let's look at what was created:
@@ -376,7 +378,6 @@ apm install company/templates/chatmodes/qa-assistant.chatmode.md
 
 - `.prompt.md` - Agent workflows
 - `.instructions.md` - Context and rules
-- `.chatmode.md` - Chat mode configurations
 - `.agent.md` - Agent definitions
 
 **Installation Structure:**

docs/integrations.md

@@ -131,20 +131,25 @@ APM works natively with VSCode's Context implementation:
 
 VSCode already implements core Context concepts:
 
-- **Chat Modes**: Domain-specific chat behavior with `.chatmode.md` files in `.github/chatmodes/`
+- **Agents**: AI personas and workflows with `.agent.md` files in `.github/agents/` (legacy: `.chatmode.md` in `.github/chatmodes/`)
 - **Instructions Files**: Modular instructions with `copilot-instructions.md` and `.instructions.md` files
 - **Prompt Files**: Reusable task templates with `.prompt.md` files in `.github/prompts/`
 
-### Automatic Prompt Integration with APM
+> **Note**: APM supports both the new `.agent.md` format and legacy `.chatmode.md` format. VSCode provides Quick Fix actions to migrate from `.chatmode.md` to `.agent.md`.
 
-APM automatically integrates prompts from installed packages into VSCode's native structure:
+### Automatic Prompt and Agent Integration with APM
+
+APM automatically integrates prompts and agents from installed packages into VSCode's native structure:
 
 ```bash
 # Install APM packages - integration happens automatically
 apm install danielmeppiel/design-guidelines
 
 # Prompts are automatically integrated to:
 # .github/prompts/*-apm.prompt.md (with package metadata header)
+
+# Agents are automatically integrated to:
+# .github/agents/*-apm.agent.md (with package metadata header)
 ```
 
 **How Auto-Integration Works**:
@@ -157,13 +162,14 @@ apm install danielmeppiel/design-guidelines
 
 **Integration Flow**:
 1. Run `apm install` to fetch APM packages
-2. APM automatically creates `.github/prompts/` directory if needed
-3. Discovers `.prompt.md` files in each package
+2. APM automatically creates `.github/prompts/` and `.github/agents/` directories if needed
+3. Discovers `.prompt.md` and `.agent.md` files in each package
 4. Copies prompts to `.github/prompts/` with `-apm` suffix (e.g., `accessibility-audit-apm.prompt.md`)
-5. Adds metadata headers for version tracking
-6. Updates `.gitignore` to exclude integrated prompts
-7. VSCode automatically loads all prompts for your coding agents
-8. Run `apm uninstall` to automatically remove integrated prompts
+5. Copies agents to `.github/agents/` with `-apm` suffix (e.g., `security-apm.agent.md`)
+6. Adds metadata headers for version tracking
+7. Updates `.gitignore` to exclude integrated prompts and agents
+8. VSCode automatically loads all prompts and agents for your coding agents
+9. Run `apm uninstall` to automatically remove integrated prompts and agents
 
 **Intent-First Discovery**:
 The `-apm` suffix pattern enables natural autocomplete in VSCode:
@@ -177,21 +183,27 @@ The `-apm` suffix pattern enables natural autocomplete in VSCode:
 apm install danielmeppiel/design-guidelines
 
 # Result in VSCode:
+# Prompts:
 # .github/prompts/accessibility-audit-apm.prompt.md  ✓ Available in chat
 # .github/prompts/design-review-apm.prompt.md        ✓ Available in chat
 # .github/prompts/style-guide-check-apm.prompt.md    ✓ Available in chat
 
+# Agents:
+# .github/agents/design-reviewer-apm.agent.md        ✓ Available as chat mode
+# .github/agents/accessibility-expert-apm.agent.md   ✓ Available as chat mode
+
 # Use with natural autocomplete:
 # Type: /design
 # VSCode suggests: design-review-apm.prompt.md ✨
 ```
 
 **VSCode Native Features**:
 - All integrated prompts appear in VSCode's prompt picker
+- All integrated agents appear in VSCode's chat mode selector
 - Native chat integration with primitives
 - Seamless `/prompt` command support
 - File-pattern based instruction application
-- Chatmode support for different personas
+- Agent support for different personas and workflows
 
 ## Development Tool Integrations
 
@@ -290,7 +302,8 @@ apm install danielmeppiel/design-guidelines
 
 # GitHub Copilot automatically picks up:
 # .github/prompts/*-apm.prompt.md (integrated prompts)
-# .github/chatmodes/ (chat personalities)
+# .github/agents/*-apm.agent.md (integrated agents)
+# .github/agents/ or .github/chatmodes/ (AI personas - both formats supported)
 # .github/instructions/ (file-pattern rules)
 ```
 

docs/primitives.md

@@ -18,9 +18,9 @@ apm init my-project  # Creates complete Context scaffolding + apm.yml
 my-project/
 ├── apm.yml              # Project configuration and script definitions
 └── .apm/
-    ├── chatmodes/       # Role-based AI expertise with tool boundaries
-    │   ├── backend-dev.chatmode.md     # API development specialist
-    │   └── frontend-dev.chatmode.md    # UI development specialist
+    ├── agents/          # Role-based AI expertise with tool boundaries
+    │   ├── backend-dev.agent.md        # API development specialist
+    │   └── frontend-dev.agent.md       # UI development specialist
     ├── instructions/    # Targeted guidance by file type and domain  
     │   ├── security.instructions.md    # applyTo: "auth/**"
     │   └── testing.instructions.md     # applyTo: "**/*test*"
@@ -70,10 +70,12 @@ apm run review-copilot --param files="src/auth/"
 
 The APM CLI supports three types of primitives:
 
-- **Chatmodes** (`.chatmode.md`) - Define AI assistant personalities and behaviors
+- **Agents** (`.agent.md`) - Define AI assistant personalities and behaviors (legacy: `.chatmode.md`)
 - **Instructions** (`.instructions.md`) - Provide coding standards and guidelines for specific file types
 - **Context** (`.context.md`, `.memory.md`) - Supply background information and project context
 
+> **Note**: Both `.agent.md` (new format) and `.chatmode.md` (legacy format) are fully supported. VSCode provides Quick Fix actions to help migrate from `.chatmode.md` to `.agent.md`.
+
 ## File Structure
 
 ### Supported Locations
@@ -83,7 +85,9 @@ APM discovers primitives in these locations:
 ```
 # APM-native structure
 .apm/
-├── chatmodes/           # AI assistant definitions
+├── agents/             # AI assistant definitions (new format)
+│   └── *.agent.md
+├── chatmodes/          # AI assistant definitions (legacy format)
 │   └── *.chatmode.md
 ├── instructions/        # Coding standards and guidelines  
 │   └── *.instructions.md
@@ -94,12 +98,15 @@ APM discovers primitives in these locations:
 
 # VSCode-compatible structure  
 .github/
-├── chatmodes/          # VSCode Copilot chatmodes
+├── agents/             # VSCode Copilot agents (new format)
+│   └── *.agent.md
+├── chatmodes/          # VSCode Copilot chatmodes (legacy format)
 │   └── *.chatmode.md
 └── instructions/       # VSCode Copilot instructions
     └── *.instructions.md
 
 # Generic files (anywhere in project)
+*.agent.md
 *.chatmode.md
 *.instructions.md
 *.context.md
@@ -142,10 +149,10 @@ Use ${input:auth_method} with ${input:session_duration} sessions
 Review [security standards](../context/security.context.md) before implementation
 ```
 
-### Chat Modes (.chatmode.md)
+### Agents (.agent.md, legacy: .chatmode.md)
 **Agent Specialization Layer** - AI assistant personalities with tool boundaries
 
-Chat modes create specialized AI assistants focused on specific domains. They define expertise areas, communication styles, and available tools.
+Agents create specialized AI assistants focused on specific domains. They define expertise areas, communication styles, and available tools.
 
 ```yaml
 ---
@@ -157,6 +164,8 @@ You are a senior backend engineer with 10+ years experience in API development.
 Focus on security, performance, and maintainable architecture patterns.
 ```
 
+> **File Format**: Use `.agent.md` for new files. Legacy `.chatmode.md` files continue to work and can be migrated using VSCode Quick Fix actions.
+
 ### Context (.context.md)
 **Knowledge Management Layer** - Optimized project information for AI consumption
 
@@ -172,15 +181,14 @@ Context files package project knowledge, architectural decisions, and team stand
 
 ## Primitive Types
 
-### Chatmodes
+### Agents
 
-Chatmodes define AI assistant personalities and specialized behaviors for different development tasks.
+Agents define AI assistant personalities and specialized behaviors for different development tasks.
 
-**Format:** `.chatmode.md`
+**Format:** `.agent.md` (new) or `.chatmode.md` (legacy)
 
 **Frontmatter:**
-- `description` (required) - Clear explanation of the chatmode purpose
-- `applyTo` (optional) - Glob pattern for file targeting (e.g., `"**/*.{py,js}"`)
+- `description` (required) - Clear explanation of the agent purpose
 - `author` (optional) - Creator information
 - `version` (optional) - Version string
 
@@ -189,7 +197,6 @@ Chatmodes define AI assistant personalities and specialized behaviors for differ
 ---
 description: AI pair programming assistant for code review
 author: Development Team
-applyTo: "**/*.{py,js,ts}"
 version: "1.0.0"
 ---
 
@@ -312,32 +319,13 @@ Team information (`.apm/memory/team-contacts.memory.md`):
 
 ## Discovery and Parsing
 
-The APM CLI automatically discovers and parses all primitive files in your project:
-
-```python
-from apm_cli.primitives import discover_primitives
-
-# Discover all primitives in current directory
-collection = discover_primitives()
-
-print(f"Found {collection.count()} primitives:")
-print(f"  Chatmodes: {len(collection.chatmodes)}")
-print(f"  Instructions: {len(collection.instructions)}")  
-print(f"  Contexts: {len(collection.contexts)}")
-
-# Access individual primitives
-for chatmode in collection.chatmodes:
-    print(f"Chatmode: {chatmode.name}")
-    print(f"  Description: {chatmode.description}")
-    if chatmode.apply_to:
-        print(f"  Applies to: {chatmode.apply_to}")
-```
+The APM CLI automatically discovers and parses all primitive files in your project.
 
 ## Validation
 
 All primitives are automatically validated during discovery:
 
-- **Chatmodes**: Must have description and content
+- **Agents**: Must have description and content (supports both `.agent.md` and `.chatmode.md`)
 - **Instructions**: Must have description, applyTo pattern, and content
 - **Context**: Must have content (description optional)
 
@@ -347,7 +335,7 @@ Invalid files are skipped with warning messages, allowing valid primitives to co
 
 ### 1. Clear Naming
 Use descriptive names that indicate purpose:
-- `code-review-assistant.chatmode.md`
+- `code-review-assistant.agent.md`
 - `python-documentation.instructions.md`
 - `team-contacts.md`
 
@@ -364,9 +352,9 @@ Keep primitives in version control alongside your code. Use semantic versioning
 Use the structured `.apm/` directories for better organization:
 ```
 .apm/
-├── chatmodes/
-│   ├── code-reviewer.chatmode.md
-│   └── documentation-writer.chatmode.md
+├── agents/
+│   ├── code-reviewer.agent.md
+│   └── documentation-writer.agent.md
 ├── instructions/
 │   ├── python-style.instructions.md
 │   └── typescript-conventions.instructions.md
@@ -385,13 +373,13 @@ Use the structured `.apm/` directories for better organization:
 For VSCode Copilot compatibility, place files in `.github/` directories:
 ```
 .github/
-├── chatmodes/
-│   └── assistant.chatmode.md
+├── agents/
+│   └── assistant.agent.md
 └── instructions/
     └── coding-standards.instructions.md
 ```
 
-These files follow the same format and will be discovered alongside APM-specific primitives.
+These files follow the same format and will be discovered alongside APM-specific primitives. 
 
 ## Error Handling
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "apm-cli"
-version = "0.5.3"
+version = "0.5.4"
 description = "MCP configuration tool"
 readme = "README.md"
 requires-python = ">=3.9"