ma-agents 2.16.0 → 2.16.2

package/.agent/workflows/bmad-help.md

@@ -0,0 +1,10 @@
+---
+name: 'help'
+description: 'Analyzes what is done and the users query and offers advice on what to do next. Use if user says what should I do next or what do I do now'
+---
+
+# help
+
+Read the entire task file at: {project-root}/_bmad/core/tasks/help.md
+
+Follow all instructions in the task file exactly as written.

package/.agent/workflows/bmad-index-docs.md

@@ -0,0 +1,10 @@
+---
+name: 'index-docs'
+description: 'Generates or updates an index.md to reference all docs in the folder. Use if user requests to create or update an index of all files in a specific folder'
+---
+
+# index-docs
+
+Read the entire task file at: {project-root}/_bmad/core/tasks/index-docs.xml
+
+Follow all instructions in the task file exactly as written.

package/.agent/workflows/bmad-party-mode.md

@@ -0,0 +1,6 @@
+---
+name: 'party-mode'
+description: 'Orchestrates group discussions between all installed BMAD agents, enabling natural multi-agent conversations. Use when user requests party mode.'
+---
+
+IT IS CRITICAL THAT YOU FOLLOW THIS COMMAND: LOAD the FULL {project-root}/_bmad/core/workflows/party-mode/workflow.md, READ its entire contents and follow its directions exactly!

package/.agent/workflows/bmad-review-adversarial-general.md

@@ -0,0 +1,10 @@
+---
+name: 'review-adversarial-general'
+description: 'Perform a Cynical Review and produce a findings report. Use when the user requests a critical review of something'
+---
+
+# review-adversarial-general
+
+Read the entire task file at: {project-root}/_bmad/core/tasks/review-adversarial-general.xml
+
+Follow all instructions in the task file exactly as written.

package/.agent/workflows/bmad-review-edge-case-hunter.md

@@ -0,0 +1,10 @@
+---
+name: 'review-edge-case-hunter'
+description: 'Walk every branching path and boundary condition in content, report only unhandled edge cases. Orthogonal to adversarial review - method-driven not attitude-driven.'
+---
+
+# review-edge-case-hunter
+
+Read the entire task file at: {project-root}/_bmad/core/tasks/review-edge-case-hunter.xml
+
+Follow all instructions in the task file exactly as written.

package/.agent/workflows/bmad-shard-doc.md

@@ -0,0 +1,10 @@
+---
+name: 'shard-doc'
+description: 'Splits large markdown documents into smaller, organized files based on level 2 (default) sections. Use if the user says perform shard document'
+---
+
+# shard-doc
+
+Read the entire task file at: {project-root}/_bmad/core/tasks/shard-doc.xml
+
+Follow all instructions in the task file exactly as written.

package/README.md

@@ -2,17 +2,23 @@
 
 A universal NPX tool to install AI coding agent skills. Write skills once, install them across Claude Code, Gemini, Copilot, Cline, Cursor, and Kilocode.
 
-## Quick Start
+## Installation & Usage
 
+`ma-agents` is designed to be run via `npx` in the root of your project.
+
+### 1. Interactive Wizard (Recommended)
+The wizard is the easiest way to set up or update your environment.
 ```bash
-# Interactive wizard (Install All / Custom Select / Update / Uninstall)
 npx ma-agents
+```
 
-# Direct install
-npx ma-agents install code-review claude-code
+### 2. Direct Command Line
+```bash
+# Install specific skills to specific agents
+npx ma-agents install code-review claude-code copilot
 
-# Install a skill to multiple agents at once
-npx ma-agents install code-review claude-code copilot cline
+# Global installation (user-level)
+npx ma-agents install code-review claude-code --global
 ```
 
 ## How It Works
@@ -43,18 +49,19 @@ skills/code-review/
 
 | Agent | Project Path | Template | Instruction File |
 |-------|-------------|----------|------------------|
-| Claude Code | `.claude/skills/` | `claude-code` | `CLAUDE.md` |
-| Google Gemini | `.gemini/skills/` | `generic` | - |
-| GitHub Copilot | `.github/copilot/skills/` | `generic` | - |
-| Cursor | `.cursor/skills/` | `generic` | - |
-| Cline | `.cline/skills/` | `cline` | `.clinerules` |
-| SRE Agent (Alex) | `.sre/skills/` | `generic` | - |
-| DevOps Agent (Amit) | `.devops/skills/` | `generic` | - |
-| Cyber Analyst (Yael) | `.cyber/skills/` | `generic` | - |
-| Antigravity | `.antigravity/skills/` | `generic` | - |
-| Kilocode | `.kilocode/skills/` | `generic` | - |
-
-## Available Skills (22)
+| Claude Code | `.claude/skills/` | `claude-code` | `.claude/CLAUDE.md` |
+| Google Gemini | `.gemini/skills/` | `generic` | `.gemini/gemini.md` |
+| GitHub Copilot | `.github/copilot/skills/` | `generic` | `.github/copilot/copilot.md` |
+| Cursor | `.cursor/skills/` | `generic` | `.cursor/cursor.md` |
+| Kilocode | `.kilocode/skills/` | `generic` | `.kilocode/kilocode.md` |
+| Cline | `.cline/skills/` | `cline` | `.cline/clinerules.md` |
+| SRE Agent (Alex) | `_bmad/skills/` | `generic` | `_bmad/bmm/agents/sre.md` |
+| DevOps Agent (Amit) | `_bmad/skills/` | `generic` | `_bmad/bmm/agents/devops.md` |
+| Cyber Analyst (Yael) | `_bmad/skills/` | `generic` | `_bmad/bmm/agents/cyber.md` |
+| Joseph (MIL-STD-498) | `_bmad/skills/` | `generic` | `_bmad/bmm/agents/mil498.md` |
+| Antigravity | `_bmad/skills/` | `generic` | `_bmad/bmm/agents/antigravity.md` |
+
+## Available Skills (25)
 
 | Skill ID | Domain | Description |
 | :--- | :--- | :--- |
@@ -117,13 +124,14 @@ npx ma-agents agents                       # List supported agents
 npx ma-agents uninstall <skill> <agents>   # Direct uninstall
 ```
 
-### The Interactive Wizard
-The easiest way to manage your skills is to simply run `npx ma-agents`. The wizard will guide you through:
-- **Install All**: One-click setup for the entire 22-skill suite.
-- **Custom Select**: Granularly choose specific skills and agents.
-- **Update**: Add or remove skills from an existing installation.
-- **Clean Reinstall**: Wipe the slate and start fresh.
-- **Uninstall All**: Remove all ma-agents artifacts from the project.
+### The Update Process
+Running `ma-agents` on a project where skills are already installed triggers the **Update Flow**:
+1. **Detection**: Recognizes existing `.ma-agents.json` manifest.
+2. **Selection**: Allows you to add new skills or remove existing ones.
+3. **Synchronization**: 
+   - Re-injects the latest instructions into `CLAUDE.md`, `.clinerules`, etc.
+   - Regenerates the `MANIFEST.yaml` to reflect the current skill set.
+   - Updates BMAD-METHOD personas and workflows to the latest versions if detected.
 
 ### BMAD-METHOD Integration
 `ma-agents` features first-class integration with [BMAD-METHOD](https://docs.bmad-method.org/) to provide advanced orchestration and specialized personas.
@@ -147,6 +155,10 @@ The easiest way to manage your skills is to simply run `npx ma-agents`. The wiza
    - **Focus**: Cyber immunity, security auditing, and vulnerability management.
    - **Capabilities**: Immunity estimation (scoring), Vault secret management, and PKI automation.
    - **Integration**: Orchestrates ma-agents security skills for deep scans.
+4. **Joseph (MIL-STD-498)**:
+   - **Focus**: Technical standards compliance and military document generation.
+   - **Capabilities**: Document Data Descriptions (DIDs), requirements traceability, and complex specification writing.
+   - **Workflows**: SRS, SSS, and SSDD generation with strict structural validation.
 
 #### Operational Workflows
 The integration includes a suite of specialized playbooks:
@@ -326,9 +338,13 @@ ma-agents/
 │   └── cli.js                  # CLI entry point (wizard + commands)
 ├── lib/
 │   ├── agents.js               # Agent configurations and paths
-│   └── installer.js            # Skill discovery, frontmatter injection, installation
+│   ├── installer.js            # Skill discovery and installation logic
+│   ├── bmad.js                 # BMAD-METHOD integration and injection logic
+│   ├── bmad-customizations/    # BMAD persona templates (.md) and YAML configs
+│   ├── bmad-workflows/         # Specialized BMAD playbooks (SRE, Cyber, etc.)
+│   └── mil498-templates/       # MIL-STD-498 DID library (SRS, SSS, SSDD, etc.)
 ├── skills/
-│   ├── code-review/            # 22 bundled skills across 5 domains
+│   ├── code-review/            # 25 bundled skills across 5 domains
 │   ├── commit-message/
 │   ├── create-hardened-docker-skill/
 │   ├── git-workflow-skill/

package/bin/cli.js

@@ -52,8 +52,8 @@ function showAgents() {
   const agents = listAgents();
   console.log(chalk.bold('\n Supported Agents:\n'));
 
-  const ideAgents = agents.filter(a => !['bmm-sre', 'bmm-devops', 'bmm-cyber', 'bmm-mil498'].includes(a.id));
-  const bmadAgents = agents.filter(a => ['bmm-sre', 'bmm-devops', 'bmm-cyber', 'bmm-mil498'].includes(a.id));
+  const ideAgents = agents.filter(a => a.category !== 'bmad');
+  const bmadAgents = agents.filter(a => a.category === 'bmad');
 
   console.log(chalk.bold.yellow('  AI Coding Assistants:'));
   ideAgents.forEach(agent => {
@@ -235,8 +235,8 @@ async function installWizard(preselectedSkill, preselectedAgents, customPath, fo
 
   // Step 2: Select agents
   if (selectedAgentIds.length === 0 || isUpdate) {
-    const ideAgents = agents.filter(a => !['bmm-sre', 'bmm-devops', 'bmm-cyber', 'bmm-mil498'].includes(a.id));
-    const bmadAgents = agents.filter(a => ['bmm-sre', 'bmm-devops', 'bmm-cyber', 'bmm-mil498'].includes(a.id));
+    const ideAgents = agents.filter(a => a.category !== 'bmad');
+    const bmadAgents = agents.filter(a => a.category === 'bmad');
 
     // 2.1 Coding Assistants
     const { ideChosen } = await prompts({
@@ -320,7 +320,7 @@ async function installWizard(preselectedSkill, preselectedAgents, customPath, fo
         if (success) {
           console.log(chalk.green(' BMAD-METHOD installed successfully!'));
           console.log(chalk.cyan(' Applying ma-agents customizations...'));
-          await bmad.applyCustomizations();
+          await bmad.applyCustomizations(process.cwd(), ['bmm', 'bmb'], bmadTools, selectedAgentIds);
         }
       }
     } else {
@@ -338,7 +338,7 @@ async function installWizard(preselectedSkill, preselectedAgents, customPath, fo
         if (success) {
           console.log(chalk.green(' BMAD-METHOD updated successfully!'));
           console.log(chalk.cyan(' Re-applying ma-agents customizations...'));
-          await bmad.applyCustomizations();
+          await bmad.applyCustomizations(process.cwd(), ['bmm', 'bmb'], bmadTools, selectedAgentIds);
         }
       }
     }
@@ -366,17 +366,43 @@ async function installWizard(preselectedSkill, preselectedAgents, customPath, fo
 
   // Step 5: Execution
   if (isUpdate) {
-    // Identify removals
-    const currentlyInstalled = new Set();
-    existingStatus.forEach(entry => Object.keys(entry.skills).forEach(id => currentlyInstalled.add(id)));
+    // Build a map: skillId -> set of agent IDs that originally had it installed
+    const originalAgentsBySkill = new Map();
+    const originalAllAgentIds = new Set();
+    existingStatus.forEach(entry => {
+      originalAllAgentIds.add(entry.agent.id);
+      Object.keys(entry.skills).forEach(skillId => {
+        if (!originalAgentsBySkill.has(skillId)) {
+          originalAgentsBySkill.set(skillId, new Set());
+        }
+        originalAgentsBySkill.get(skillId).add(entry.agent.id);
+      });
+    });
 
     const finalSkills = new Set(selectedSkillIds);
-    const toRemove = [...currentlyInstalled].filter(id => !finalSkills.has(id));
+
+    // Skills to fully remove (deselected from skill list)
+    const toRemove = [...originalAgentsBySkill.keys()].filter(id => !finalSkills.has(id));
 
     if (toRemove.length > 0) {
       console.log(chalk.gray(`\n  Cleaning up ${toRemove.length} removed skills...`));
       for (const skillId of toRemove) {
-        await uninstallSkill(skillId, selectedAgentIds, installPath, 'project');
+        // Use the ORIGINAL agent IDs, not the new selection
+        const originalAgents = [...originalAgentsBySkill.get(skillId)];
+        await uninstallSkill(skillId, originalAgents, installPath, 'project');
+      }
+    }
+
+    // Also handle agents that were deselected: uninstall their skills
+    const deselectedAgents = [...originalAllAgentIds].filter(id => !selectedAgentIds.includes(id));
+
+    if (deselectedAgents.length > 0) {
+      console.log(chalk.gray(`\n  Removing skills from ${deselectedAgents.length} deselected agents...`));
+      for (const [skillId, agentSet] of originalAgentsBySkill) {
+        const agentsToRemoveFrom = deselectedAgents.filter(id => agentSet.has(id));
+        if (agentsToRemoveFrom.length > 0) {
+          await uninstallSkill(skillId, agentsToRemoveFrom, installPath, 'project');
+        }
       }
     }
   }

package/lib/agents.js

@@ -6,6 +6,7 @@ const path = require('path');
  * Each agent has:
  * - id: unique identifier
  * - name: display name
+ * - category: 'ide' for AI coding assistants, 'bmad' for BMAD-METHOD agents
  * - description: brief description
  * - getProjectPath: function that returns the project-level skills directory (relative to cwd)
  * - getGlobalPath: function that returns the global/user-level skills directory
@@ -18,6 +19,7 @@ const agents = [
     id: 'claude-code',
     name: 'Claude Code',
     version: '1.0.0',
+    category: 'ide',
     description: 'Anthropic Claude Code CLI',
     getProjectPath: () => path.join(process.cwd(), '.claude', 'skills'),
     getGlobalPath: () => {
@@ -38,6 +40,7 @@ const agents = [
     id: 'gemini',
     name: 'Google Gemini',
     version: '1.0.0',
+    category: 'ide',
     description: 'Google Gemini Code Assist',
     getProjectPath: () => path.join(process.cwd(), '.gemini', 'skills'),
     getGlobalPath: () => {
@@ -58,6 +61,7 @@ const agents = [
     id: 'copilot',
     name: 'GitHub Copilot',
     version: '1.0.0',
+    category: 'ide',
     description: 'GitHub Copilot Agent Mode',
     getProjectPath: () => path.join(process.cwd(), '.github', 'copilot', 'skills'),
     getGlobalPath: () => {
@@ -78,6 +82,7 @@ const agents = [
     id: 'kilocode',
     name: 'Kilocode',
     version: '1.0.0',
+    category: 'ide',
     description: 'Kilocode AI Assistant',
     getProjectPath: () => path.join(process.cwd(), '.kilocode', 'skills'),
     getGlobalPath: () => {
@@ -98,6 +103,7 @@ const agents = [
     id: 'cline',
     name: 'Cline',
     version: '1.0.0',
+    category: 'ide',
     description: 'Cline AI Assistant',
     getProjectPath: () => path.join(process.cwd(), '.cline', 'skills'),
     getGlobalPath: () => {
@@ -123,6 +129,7 @@ const agents = [
     id: 'cursor',
     name: 'Cursor',
     version: '1.0.0',
+    category: 'ide',
     description: 'Cursor AI Editor',
     getProjectPath: () => path.join(process.cwd(), '.cursor', 'skills'),
     getGlobalPath: () => {
@@ -143,6 +150,7 @@ const agents = [
     id: 'bmm-sre',
     name: 'SRE Agent',
     version: '1.0.0',
+    category: 'bmad',
     description: 'Specialized SRE Agent for BMAD-METHOD',
     getProjectPath: () => path.join(process.cwd(), '_bmad', 'skills'),
     getGlobalPath: () => {
@@ -163,8 +171,9 @@ const agents = [
     id: 'antigravity',
     name: 'Antigravity',
     version: '1.0.0',
+    category: 'ide',
     description: 'Google Deepmind Antigravity Agent',
-    getProjectPath: () => path.join(process.cwd(), '_bmad', 'skills'),
+    getProjectPath: () => path.join(process.cwd(), '.antigravity', 'skills'),
     getGlobalPath: () => {
       const platform = os.platform();
       if (platform === 'win32') {
@@ -177,12 +186,13 @@ const agents = [
     },
     fileExtension: '.md',
     template: 'generic',
-    instructionFiles: ['_bmad/bmm/agents/antigravity.md']
+    instructionFiles: ['.antigravity/antigravity.md']
   },
   {
     id: 'bmm-devops',
     name: 'DevOps Agent',
     version: '1.0.0',
+    category: 'bmad',
     description: 'Specialized DevOps Agent for BMAD-METHOD',
     getProjectPath: () => path.join(process.cwd(), '_bmad', 'skills'),
     getGlobalPath: () => {
@@ -203,6 +213,7 @@ const agents = [
     id: 'bmm-cyber',
     name: 'Cyber Analyst',
     version: '1.0.0',
+    category: 'bmad',
     description: 'Specialized Cyber Security Analyst (Yael) for BMAD-METHOD',
     getProjectPath: () => path.join(process.cwd(), '_bmad', 'skills'),
     getGlobalPath: () => {
@@ -221,8 +232,9 @@ const agents = [
   },
   {
     id: 'bmm-mil498',
-    name: 'Joseph',
+    name: 'MIL-STD-498 Expert',
     version: '1.0.0',
+    category: 'bmad',
     description: 'MIL-STD-498 Documentation Expert',
     getProjectPath: () => path.join(process.cwd(), '_bmad', 'skills'),
     getGlobalPath: () => {
@@ -249,7 +261,12 @@ function getAllAgents() {
   return agents;
 }
 
+function getAgentsByCategory(category) {
+  return agents.filter(a => a.category === category);
+}
+
 module.exports = {
   getAgent,
-  getAllAgents
+  getAllAgents,
+  getAgentsByCategory
 };

package/lib/bmad-customizations/bmm-mil498.customize.yaml

@@ -15,16 +15,19 @@ persona:
 menu:
   - trigger: bmad-mil-generate-srs
     workflow: "bmm/workflows/mil498/bmad-mil-generate-srs.md"
-    description: "Generate SRS Document"
+    description: "Generate SRS (Software Requirements Specification)"
   - trigger: bmad-mil-generate-sdd
     workflow: "bmm/workflows/mil498/bmad-mil-generate-sdd.md"
-    description: "Generate SDD Document"
-  - trigger: bmad-mil-generate-stp
-    workflow: "bmm/workflows/mil498/bmad-mil-generate-stp.md"
-    description: "Generate STP Document"
-  - trigger: bmad-mil-generate-ocd
-    workflow: "bmm/workflows/mil498/bmad-mil-generate-ocd.md"
-    description: "Generate OCD Document"
+    description: "Generate SDD (Software Design Description)"
   - trigger: bmad-mil-generate-sdp
     workflow: "bmm/workflows/mil498/bmad-mil-generate-sdp.md"
-    description: "Generate SDP Document"
+    description: "Generate SDP (Software Development Plan)"
+  - trigger: bmad-mil-generate-ocd
+    workflow: "bmm/workflows/mil498/bmad-mil-generate-ocd.md"
+    description: "Generate OCD (Operational Concept Description)"
+  - trigger: bmad-mil-generate-sss
+    workflow: "bmm/workflows/mil498/bmad-mil-generate-sss.md"
+    description: "Generate SSS (System/Subsystem Specification)"
+  - trigger: bmad-mil-generate-std
+    workflow: "bmm/workflows/mil498/bmad-mil-generate-std.md"
+    description: "Generate STD (Software Test Description)"

package/lib/bmad-customizations/mil498.md

@@ -62,9 +62,12 @@ You must fully embody this agent's persona and follow all activation instruction
 <menu>
     <item cmd="MH">[MH] Redisplay Menu Help</item>
     <item cmd="CH">[CH] Chat with Joseph about MIL-STD-498</item>
-    <item cmd="GS" workflow="{project-root}/_bmad/bmm/workflows/mil498/bmad-mil-generate-srs.md">[GS] Generate SRS: Generate a Software Requirements Specification</item>
-    <item cmd="GD" workflow="{project-root}/_bmad/bmm/workflows/mil498/bmad-mil-generate-sdd.md">[GD] Generate SDD: Generate a Software Design Description</item>
-    <item cmd="GT" workflow="{project-root}/_bmad/bmm/workflows/mil498/bmad-mil-generate-stp.md">[GT] Generate STP: Generate a Software Test Plan</item>
+    <item cmd="GS" workflow="{project-root}/_bmad/bmm/workflows/mil498/bmad-mil-generate-srs.md">[GS] Generate SRS: Software Requirements Specification</item>
+    <item cmd="GD" workflow="{project-root}/_bmad/bmm/workflows/mil498/bmad-mil-generate-sdd.md">[GD] Generate SDD: Software Design Description</item>
+    <item cmd="GP" workflow="{project-root}/_bmad/bmm/workflows/mil498/bmad-mil-generate-sdp.md">[GP] Generate SDP: Software Development Plan</item>
+    <item cmd="GO" workflow="{project-root}/_bmad/bmm/workflows/mil498/bmad-mil-generate-ocd.md">[GO] Generate OCD: Operational Concept Description</item>
+    <item cmd="SS" workflow="{project-root}/_bmad/bmm/workflows/mil498/bmad-mil-generate-sss.md">[SS] Generate SSS: System/Subsystem Specification</item>
+    <item cmd="GT" workflow="{project-root}/_bmad/bmm/workflows/mil498/bmad-mil-generate-std.md">[GT] Generate STD: Software Test Description</item>
     <item cmd="DA">[DA] Dismiss Agent</item>
 </menu>
 </agent>

package/lib/bmad.js

@@ -42,6 +42,8 @@ async function updateBmad(modules = ['bmm', 'bmb'], tools = [], projectRoot = pr
 
     if (tools && tools.length > 0) {
         command += ` --tools ${tools.join(',')}`;
+    } else {
+        command += ' --tools none';
     }
 
     console.log(chalk.gray(`  Running: ${command}`));
@@ -54,7 +56,7 @@ async function updateBmad(modules = ['bmm', 'bmb'], tools = [], projectRoot = pr
     }
 }
 
-async function applyCustomizations(projectRoot = process.cwd()) {
+async function applyCustomizations(projectRoot = process.cwd(), modules = ['bmm', 'bmb'], tools = [], selectedAgentIds = []) {
     const sourceDir = path.join(__dirname, 'bmad-customizations');
     const workflowSourceDir = path.join(__dirname, 'bmad-workflows');
     const configTargetDir = path.join(projectRoot, CONFIG_DIR);
@@ -63,26 +65,41 @@ async function applyCustomizations(projectRoot = process.cwd()) {
     const templateSourceDir = path.join(__dirname, 'mil498-templates');
     const templateTargetDir = path.join(projectRoot, BMAD_DIR, 'bmm', 'templates', 'mil498');
 
-    // 1. Apply YAML customizations
+    // Mapping from BMAD agent IDs to their .md template filenames
+    const agentMdMap = {
+        'bmm-sre': 'sre.md',
+        'bmm-devops': 'devops.md',
+        'bmm-cyber': 'cyber.md',
+        'bmm-mil498': 'mil498.md'
+    };
+
+    // 1. Apply YAML customizations (filtered by selected agents)
     if (fs.existsSync(sourceDir)) {
         await fs.ensureDir(configTargetDir);
         const files = await fs.readdir(sourceDir);
         for (const file of files) {
             if (file.endsWith('.customize.yaml')) {
-                await fs.copy(path.join(sourceDir, file), path.join(configTargetDir, file));
-                console.log(chalk.cyan(`    + Applied customization: ${file}`));
+                const agentId = file.replace('.customize.yaml', '');
+                // Always copy generic; filter others by selected agents
+                if (agentId === 'generic' || selectedAgentIds.length === 0 || selectedAgentIds.includes(agentId)) {
+                    await fs.copy(path.join(sourceDir, file), path.join(configTargetDir, file));
+                    console.log(chalk.cyan(`    + Applied customization: ${file}`));
+                }
             }
         }
     }
 
-    // 2. Apply detailed agent templates (.md files)
+    // 2. Apply detailed agent templates (.md files, filtered by selected agents)
     if (fs.existsSync(sourceDir)) {
         await fs.ensureDir(agentTargetDir);
         const files = await fs.readdir(sourceDir);
         for (const file of files) {
             if (file.endsWith('.md')) {
-                await fs.copy(path.join(sourceDir, file), path.join(agentTargetDir, file));
-                console.log(chalk.cyan(`    + Applied agent template: ${file}`));
+                const matchingAgentId = Object.entries(agentMdMap).find(([, mdFile]) => mdFile === file)?.[0];
+                if (!matchingAgentId || selectedAgentIds.length === 0 || selectedAgentIds.includes(matchingAgentId)) {
+                    await fs.copy(path.join(sourceDir, file), path.join(agentTargetDir, file));
+                    console.log(chalk.cyan(`    + Applied agent template: ${file}`));
+                }
             }
         }
     }
@@ -102,13 +119,99 @@ async function applyCustomizations(projectRoot = process.cwd()) {
     }
 
     // Recompile agents to apply changes
-    const command = 'npx bmad-method install --yes';
+    let command = 'npx bmad-method install --yes';
+    if (modules && modules.length > 0) {
+        command += ` --modules ${modules.join(',')}`;
+    }
+    if (tools && tools.length > 0) {
+        command += ` --tools ${tools.join(',')}`;
+    } else {
+        command += ' --tools none';
+    }
     console.log(chalk.gray(`  Running: ${command}`));
     try {
         execSync(command, { stdio: 'inherit', cwd: projectRoot });
     } catch (error) {
         console.error(chalk.red(`  BMAD recompile failed: ${error.message}`));
     }
+
+    // 5. Register custom workflows in BMAD CSV registries (after recompile)
+    if (selectedAgentIds.length === 0 || selectedAgentIds.includes('bmm-mil498')) {
+        await registerMilWorkflows(projectRoot);
+    }
+}
+
+/**
+ * Append MIL-STD-498 workflow entries to the BMAD CSV registries
+ * so they appear as available slash commands.
+ */
+async function registerMilWorkflows(projectRoot) {
+    const milEntries = [
+        {
+            name: 'Generate SRS', code: 'GS',
+            file: '_bmad/bmm/workflows/mil498/bmad-mil-generate-srs.md',
+            command: 'bmad-mil-generate-srs',
+            description: 'Generate a MIL-STD-498 Software Requirements Specification from BMAD project artifacts'
+        },
+        {
+            name: 'Generate SDD', code: 'GD',
+            file: '_bmad/bmm/workflows/mil498/bmad-mil-generate-sdd.md',
+            command: 'bmad-mil-generate-sdd',
+            description: 'Generate a MIL-STD-498 Software Design Description from architecture and design docs'
+        },
+        {
+            name: 'Generate SDP', code: 'GP',
+            file: '_bmad/bmm/workflows/mil498/bmad-mil-generate-sdp.md',
+            command: 'bmad-mil-generate-sdp',
+            description: 'Generate a MIL-STD-498 Software Development Plan from project planning artifacts'
+        },
+        {
+            name: 'Generate OCD', code: 'GO',
+            file: '_bmad/bmm/workflows/mil498/bmad-mil-generate-ocd.md',
+            command: 'bmad-mil-generate-ocd',
+            description: 'Generate a MIL-STD-498 Operational Concept Description from PRD and architecture'
+        },
+        {
+            name: 'Generate SSS', code: 'SS',
+            file: '_bmad/bmm/workflows/mil498/bmad-mil-generate-sss.md',
+            command: 'bmad-mil-generate-sss',
+            description: 'Generate a MIL-STD-498 System/Subsystem Specification from project requirements'
+        },
+        {
+            name: 'Generate STD', code: 'GT',
+            file: '_bmad/bmm/workflows/mil498/bmad-mil-generate-std.md',
+            command: 'bmad-mil-generate-std',
+            description: 'Generate a MIL-STD-498 Software Test Description from epics stories and architecture'
+        }
+    ];
+
+    // Append to module-help.csv
+    const moduleHelpPath = path.join(projectRoot, BMAD_DIR, 'bmm', 'module-help.csv');
+    if (fs.existsSync(moduleHelpPath)) {
+        let content = await fs.readFile(moduleHelpPath, 'utf-8');
+        for (const entry of milEntries) {
+            if (!content.includes(entry.command)) {
+                const row = `bmm,anytime,${entry.name},${entry.code},,${entry.file},${entry.command},false,mil498,Create Mode,${entry.description},planning_artifacts,document,`;
+                content = content.trimEnd() + '\n' + row + '\n';
+            }
+        }
+        await fs.writeFile(moduleHelpPath, content, 'utf-8');
+        console.log(chalk.cyan(`    + Registered MIL-STD-498 workflows in module-help.csv`));
+    }
+
+    // Append to bmad-help.csv
+    const bmadHelpPath = path.join(projectRoot, BMAD_DIR, '_config', 'bmad-help.csv');
+    if (fs.existsSync(bmadHelpPath)) {
+        let content = await fs.readFile(bmadHelpPath, 'utf-8');
+        for (const entry of milEntries) {
+            if (!content.includes(entry.command)) {
+                const row = `bmm,anytime,${entry.name},${entry.code},,${entry.file},${entry.command},false,mil498,bmad:MIL-STD-498 compliance:agent:mil498,Joseph,📜 MIL-STD-498 Expert,Create Mode,${entry.description},planning_artifacts,document`;
+                content = content.trimEnd() + '\n' + row + '\n';
+            }
+        }
+        await fs.writeFile(bmadHelpPath, content, 'utf-8');
+        console.log(chalk.cyan(`    + Registered MIL-STD-498 workflows in bmad-help.csv`));
+    }
 }
 
 module.exports = {