superkit-mcp-server 1.2.2 → 1.2.4

package/SUPERKIT.md

@@ -125,7 +125,7 @@ cat skills/session-resume/SKILL.md
 
 **BEFORE** solving a new problem:
 ```bash
-./scripts/compound-search.sh "{keywords}"
+Call MCP `call_tool_compound_manager` { action: "search", terms: ["{keywords}"] }
 ```
 
 If solution found → Apply it, do not reinvent the wheel!
@@ -145,7 +145,7 @@ If solution found → Apply it, do not reinvent the wheel!
 
 Run daily:
 ```bash
-./scripts/compound-dashboard.sh
+Call MCP `call_tool_compound_manager` { action: "dashboard" }
 ```
 **Target**: Grade B or higher
 

package/agents/security-auditor.md

@@ -145,10 +145,11 @@ Is it actively exploited (EPSS >0.5)?
 
 ## Validation
 
-After your review, run the validation script:
+After your review, validate with project-specific checks:
 
 ```bash
-python scripts/security_scan.py <project_path> --output summary
+# Use your project's linting/security tools (e.g., npm audit, semgrep, bandit)
+npm audit --production
 ```
 
 This validates that security principles were correctly applied.

package/build/index.js

@@ -293,25 +293,34 @@ server.setRequestHandler(GetPromptRequestSchema, async (request) => {
     try {
         const content = await fs.readFile(safePath, "utf-8");
         const parsed = toml.parse(content);
-        const promptText = parsed?.prompt || `Execute the ${promptName} command.`;
+        let promptText = parsed?.prompt || `Execute the ${promptName} command.`;
+        // Resolve @{path} includes from super-kit package root
+        const includePattern = /@\{([^}]+)\}/g;
+        let match;
+        while ((match = includePattern.exec(promptText)) !== null) {
+            const includePath = match[1];
+            const resolvedPath = getSafePath(superKitRoot, includePath);
+            if (resolvedPath) {
+                try {
+                    const includeContent = await fs.readFile(resolvedPath, "utf-8");
+                    promptText = promptText.replace(match[0], includeContent);
+                }
+                catch {
+                    promptText = promptText.replace(match[0], `[File not found: ${includePath}]`);
+                }
+            }
+        }
         // Load SUPERKIT.md for systematic inclusion
         const superKitPath = path.join(superKitRoot, "SUPERKIT.md");
         const superKitContent = await fs.readFile(superKitPath, "utf-8");
         return {
             description: parsed?.description || `Loaded command: ${promptName}`,
             messages: [
-                {
-                    role: "system", // Try standard system role if supported by the client
-                    content: {
-                        type: "text",
-                        text: superKitContent,
-                    },
-                },
                 {
                     role: "user",
                     content: {
                         type: "text",
-                        text: promptText,
+                        text: `[SYSTEM INSTRUCTIONS - Follow these strictly]\n\n${superKitContent}\n\n[USER TASK]\n\n${promptText}`,
                     },
                 },
             ],

package/build/tools/__tests__/loggerTools.test.js

@@ -17,7 +17,7 @@ describe('Logger Tools', () => {
         vi.setSystemTime(new Date('2026-03-04T00:00:00Z'));
         const result = await logSkill('test-skill', 'manual', 'context', tempDir);
         expect(result).toBe('Successfully logged skill usage for test-skill');
-        const logFile = path.join(tempDir, '.agent', 'logs', 'skill_usage.log');
+        const logFile = path.join(tempDir, 'docs', 'agents', 'logs', 'skill_usage.log');
         const content = await fs.readFile(logFile, 'utf-8');
         expect(content).toContain('2026-03-04T00:00:00Z|test-skill|manual|context\n');
         vi.useRealTimers();
@@ -27,7 +27,7 @@ describe('Logger Tools', () => {
         vi.setSystemTime(new Date('2026-03-04T00:00:00Z'));
         const result = await logWorkflow('test-workflow', 'session-123', tempDir);
         expect(result).toBe('Successfully logged workflow usage for test-workflow');
-        const logFile = path.join(tempDir, '.agent', 'logs', 'workflow_usage.log');
+        const logFile = path.join(tempDir, 'docs', 'agents', 'logs', 'workflow_usage.log');
         const content = await fs.readFile(logFile, 'utf-8');
         expect(content).toContain('2026-03-04T00:00:00Z|test-workflow|session-123\n');
         vi.useRealTimers();
@@ -36,13 +36,13 @@ describe('Logger Tools', () => {
         vi.useFakeTimers();
         vi.setSystemTime(new Date('2026-03-04T00:00:00Z')); // 1772582400 in seconds
         await logWorkflow('test-workflow', '', tempDir);
-        const logFile = path.join(tempDir, '.agent', 'logs', 'workflow_usage.log');
+        const logFile = path.join(tempDir, 'docs', 'agents', 'logs', 'workflow_usage.log');
         const content = await fs.readFile(logFile, 'utf-8');
         expect(content).toContain('2026-03-04T00:00:00Z|test-workflow|1772582400\n');
         vi.useRealTimers();
     });
     it('should rotate logs older than retention days', async () => {
-        const logDir = path.join(tempDir, '.agent', 'logs');
+        const logDir = path.join(tempDir, 'docs', 'agents', 'logs');
         await fs.mkdir(logDir, { recursive: true });
         // Old log line (e.g. 100 days old)
         const oldTimestamp = new Date();
@@ -61,7 +61,7 @@ describe('Logger Tools', () => {
         expect(finalContent).toContain('context2');
     });
     it('should report if no logs need rotation', async () => {
-        const logDir = path.join(tempDir, '.agent', 'logs');
+        const logDir = path.join(tempDir, 'docs', 'agents', 'logs');
         await fs.mkdir(logDir, { recursive: true });
         const newTimestamp = new Date();
         newTimestamp.setDate(newTimestamp.getDate() - 10);

package/build/tools/archTools.js

@@ -102,29 +102,16 @@ export async function validateArchitecture(projectPath = '.') {
     };
     const expSkills = getExpected('skills');
     const expWorkflows = getExpected('workflows');
-    const expScripts = getExpected('scripts');
     const expPatterns = getExpected('patterns');
-    let actSkills = 0, actWorkflows = 0, actScripts = 0, actPatterns = 0;
+    let actSkills = 0, actWorkflows = 0, actPatterns = 0;
     try {
         actSkills = (await fs.readdir(path.join(projectPath, 'skills'))).length;
     }
     catch { }
     try {
-        const wfs = await fs.readdir(path.join(projectPath, '.agent/workflows'));
+        const wfs = await fs.readdir(path.join(projectPath, 'skills', 'workflows'));
         actWorkflows = wfs.filter(f => f.endsWith('.md') && f !== 'README.md').length;
     }
-    catch {
-        // Fallback to workflows/
-        try {
-            const wfs = await fs.readdir(path.join(projectPath, 'workflows'));
-            actWorkflows = wfs.filter(f => f.endsWith('.md') && f !== 'README.md').length;
-        }
-        catch { }
-    }
-    try {
-        const scripts = await fs.readdir(path.join(projectPath, 'scripts'));
-        actScripts = scripts.filter(f => f.endsWith('.sh') || f.endsWith('.js') || f.endsWith('.ts')).length;
-    }
     catch { }
     try {
         const patternsCont = await fs.readFile(path.join(projectPath, 'docs/solutions/patterns/critical-patterns.md'), 'utf8');
@@ -141,10 +128,6 @@ export async function validateArchitecture(projectPath = '.') {
         out += `❌ Workflows mismatch: Doc says ${expWorkflows}, Found ${actWorkflows}\n`;
         fail = true;
     }
-    if (actScripts !== expScripts) {
-        out += `❌ Scripts mismatch: Doc says ${expScripts}, Found ${actScripts}\n`;
-        fail = true;
-    }
     if (actPatterns !== expPatterns) {
         out += `❌ Patterns mismatch: Doc says ${expPatterns}, Found ${actPatterns}\n`;
         fail = true;

package/build/tools/autoPreview.js

@@ -2,12 +2,12 @@ import * as fs from 'fs/promises';
 import { existsSync } from 'fs';
 import * as path from 'path';
 import { spawn, execSync } from 'child_process';
-const AGENT_DIR = path.resolve('.agent');
+const AGENT_DIR = path.resolve('docs', 'agents');
 const PID_FILE = path.join(AGENT_DIR, 'preview.pid');
 const LOG_FILE = path.join(AGENT_DIR, 'preview.log');
 export async function manageAutoPreview(action, port = 3000) {
     const root = path.resolve('.');
-    // Ensure .agent dir exists
+    // Ensure docs/agents dir exists
     if (!existsSync(AGENT_DIR)) {
         await fs.mkdir(AGENT_DIR, { recursive: true });
     }

package/build/tools/compoundTools.js

@@ -4,8 +4,8 @@ export async function compoundSearch(terms, projectPath = '.') {
     const searchDirs = ['docs/solutions', 'docs/explorations', 'docs/decisions'].map(d => path.join(projectPath, d));
     // Log usage
     const logLine = `${new Date().toISOString().replace(/\.[0-9]{3}Z$/, 'Z')}|compound-search|manual|${terms.join(',')}\n`;
-    await fs.mkdir(path.join(projectPath, '.agent', 'logs'), { recursive: true });
-    await fs.appendFile(path.join(projectPath, '.agent', 'logs', 'compound_usage.log'), logLine);
+    await fs.mkdir(path.join(projectPath, 'docs', 'agents', 'logs'), { recursive: true });
+    await fs.appendFile(path.join(projectPath, 'docs', 'agents', 'logs', 'compound_usage.log'), logLine);
     const results = new Set();
     async function searchInDir(dir) {
         try {
@@ -54,8 +54,8 @@ export async function updateSolutionRef(files, projectPath = '.') {
     const today = new Date().toISOString().split('T')[0];
     let count = 0;
     const logLine = `${new Date().toISOString().replace(/\.[0-9]{3}Z$/, 'Z')}|update-solution-ref|manual|${files.join(',')}\n`;
-    await fs.mkdir(path.join(projectPath, '.agent', 'logs'), { recursive: true });
-    await fs.appendFile(path.join(projectPath, '.agent', 'logs', 'compound_usage.log'), logLine);
+    await fs.mkdir(path.join(projectPath, 'docs', 'agents', 'logs'), { recursive: true });
+    await fs.appendFile(path.join(projectPath, 'docs', 'agents', 'logs', 'compound_usage.log'), logLine);
     let output = '';
     for (const file of files) {
         const fullPath = path.resolve(projectPath, file);

package/build/tools/docsTools.js

@@ -66,14 +66,9 @@ export async function checkDocsFreshness(skipDocs = false, projectPath = '.') {
     let warnings = 0;
     let output = `🔍 Checking documentation freshness for: ${commitMsg}\n`;
     const changedFiles = changedFilesStr.split('\n');
-    const newScripts = changedFiles.filter(f => f.startsWith('scripts/') && f !== 'scripts/README.md');
-    if (newScripts.length > 0 && !changedFiles.includes('scripts/README.md')) {
-        output += "⚠️  Scripts modified but scripts/README.md not updated.\n";
-        warnings++;
-    }
-    const newWorkflows = changedFiles.filter(f => f.startsWith('.agent/workflows/') && f !== '.agent/workflows/README.md');
-    if (newWorkflows.length > 0 && !changedFiles.includes('.agent/workflows/README.md')) {
-        output += "⚠️  Workflows modified but .agent/workflows/README.md not updated.\n";
+    const newWorkflows = changedFiles.filter(f => f.startsWith('skills/workflows/') && f !== 'skills/workflows/README.md');
+    if (newWorkflows.length > 0 && !changedFiles.includes('skills/workflows/README.md')) {
+        output += "⚠️  Workflows modified but skills/workflows/README.md not updated.\n";
         warnings++;
     }
     const codeChanged = changedFiles.some(f => /^(src|components|lib|app)\//.test(f));
@@ -91,7 +86,7 @@ export async function checkDocsFreshness(skipDocs = false, projectPath = '.') {
     return output;
 }
 export async function discoverUndocumentedFolders(projectPath = '.') {
-    const roots = ["app", "lib", "backend", "scripts", "src"];
+    const roots = ["app", "lib", "backend", "src"];
     const exclusions = ["node_modules", "__pycache__", ".git", "__tests__", "archive", ".vercel", ".next", "dist"];
     const undocumented = [];
     async function scanDir(dir, depth) {
@@ -132,7 +127,7 @@ export async function discoverUndocumentedFolders(projectPath = '.') {
     return "✅ All key folders have README documentation.";
 }
 export async function validateFolderDocs(strict = false, targetFolders = [], projectPath = '.') {
-    const coreFolders = ["src", "scripts", "docs/solutions", "docs/architecture", ".agent/workflows"];
+    const coreFolders = ["src", "docs/solutions", "docs/architecture", "skills/workflows", "agents"];
     const foldersToCheck = targetFolders.length > 0 ? targetFolders : coreFolders;
     let exitCode = 0;
     let output = "🔍 Validating hierarchical documentation...\n";

package/build/tools/loggerTools.js

@@ -1,7 +1,7 @@
 import * as fs from 'fs/promises';
 import * as path from 'path';
 function getLogDir(projectPath = '.') {
-    return path.join(projectPath, '.agent', 'logs');
+    return path.join(projectPath, 'docs', 'agents', 'logs');
 }
 export async function logSkill(skill, trigger = 'manual', context = '', projectPath = '.') {
     // Format timestamp like 2026-03-04T00:12:42Z (ISO 8601 without milliseconds)

package/build/tools/sessionManager.js

@@ -4,11 +4,18 @@ export async function manageSession(command, rootPath = '.') {
     const root = path.resolve(rootPath);
     const pkgPath = path.join(root, 'package.json');
     const getPackageInfo = async () => {
+        let name = root.split(path.sep).pop() || 'unnamed';
+        let version = '0.0.0';
+        const stack = [];
+        let scripts = [];
+        // 1. Node.js Check
         try {
             const data = await fs.readFile(pkgPath, 'utf8');
             const pkg = JSON.parse(data);
+            name = pkg.name || name;
+            version = pkg.version || version;
+            scripts = Object.keys(pkg.scripts || {});
             const allDeps = { ...(pkg.dependencies || {}), ...(pkg.devDependencies || {}) };
-            const stack = [];
             if (allDeps['next'])
                 stack.push("Next.js");
             else if (allDeps['react'])
@@ -27,16 +34,69 @@ export async function manageSession(command, rootPath = '.') {
                 stack.push("Prisma");
             if (allDeps['typescript'])
                 stack.push("TypeScript");
-            return {
-                name: pkg.name || 'unnamed',
-                version: pkg.version || '0.0.0',
-                stack,
-                scripts: Object.keys(pkg.scripts || {})
-            };
+            if (stack.length === 0)
+                stack.push("Node.js");
         }
-        catch (e) {
-            return { name: root.split(path.sep).pop() || 'unnamed', version: '0.0.0', stack: ['Generic'], scripts: [] };
+        catch { }
+        // 2. Polyglot Checks
+        try {
+            const files = await fs.readdir(root);
+            // Python
+            if (files.includes('requirements.txt') || files.includes('Pipfile') || files.includes('pyproject.toml')) {
+                if (!stack.includes("Python"))
+                    stack.push("Python");
+                if (files.includes('manage.py'))
+                    stack.push("Django");
+                if (files.includes('requirements.txt')) {
+                    const content = await fs.readFile(path.join(root, 'requirements.txt'), 'utf8');
+                    if (content.includes('flask'))
+                        stack.push("Flask");
+                    if (content.includes('fastapi'))
+                        stack.push("FastAPI");
+                    if (content.includes('django') && !stack.includes("Django"))
+                        stack.push("Django");
+                }
+            }
+            // Go
+            if (files.includes('go.mod'))
+                stack.push("Go");
+            // Rust
+            if (files.includes('Cargo.toml'))
+                stack.push("Rust");
+            // Java / Kotlin
+            if (files.includes('pom.xml'))
+                stack.push("Java (Maven)");
+            if (files.includes('build.gradle') || files.includes('build.gradle.kts'))
+                stack.push("Java/Kotlin (Gradle)");
+            // PHP
+            if (files.includes('composer.json')) {
+                if (!stack.includes("PHP"))
+                    stack.push("PHP");
+                try {
+                    const composer = JSON.parse(await fs.readFile(path.join(root, 'composer.json'), 'utf8'));
+                    const deps = { ...(composer.require || {}), ...(composer['require-dev'] || {}) };
+                    if (deps['laravel/framework'])
+                        stack.push("Laravel");
+                    if (deps['symfony/framework-bundle'])
+                        stack.push("Symfony");
+                }
+                catch { }
+            }
+            // Infrastructure
+            if (files.includes('Dockerfile') || files.includes('docker-compose.yml'))
+                stack.push("Docker");
+            if (files.some(f => f.endsWith('.tf')))
+                stack.push("Terraform");
         }
+        catch { }
+        if (stack.length === 0)
+            stack.push("Generic");
+        return {
+            name,
+            version,
+            stack: Array.from(new Set(stack)),
+            scripts
+        };
     };
     const countFiles = async (dir) => {
         let count = 0;
@@ -91,7 +151,16 @@ export async function manageSession(command, rootPath = '.') {
         output += `📁 Project: ${info.name}\n`;
         output += `📂 Path: ${root}\n`;
         output += `🏷️  Type: ${info.stack.join(', ')}\n`;
-        output += `📊 Status: Active\n\n`;
+        // Check for active todos to determine status
+        let status = 'Idle';
+        try {
+            const todos = await fs.readdir(path.join(root, 'todos'));
+            const hasActive = todos.some(f => f.endsWith('.md') && !f.includes('template') && !f.includes('archive'));
+            if (hasActive)
+                status = 'Active';
+        }
+        catch { }
+        output += `📊 Status: ${status}\n\n`;
         output += `🔧 Tech Stack:\n`;
         for (const tech of info.stack)
             output += `   • ${tech}\n`;

package/build/tools/validators/convertRules.js

@@ -135,12 +135,12 @@ async function generateSectionFile(sectionPrefix, rules, outputDir, getOutputOnl
 }
 export async function runConvertRules(projectPath = ".") {
     let report = `============================================================\n`;
-    report += `CONVERSION SCRIPT: React Best Practices -> .agent Format\n`;
+    report += `CONVERSION SCRIPT: React Best Practices -> Skills Format\n`;
     report += `============================================================\n`;
     const baseDir = path.resolve(projectPath);
     // Mimic the python logic for paths if run from anywhere, or adapt to superkit structure
     const rulesDir = path.join(baseDir, "skills", "react-best-practices", "rules");
-    const outputDir = path.join(baseDir, ".agent", "skills", "react-best-practices");
+    const outputDir = path.join(baseDir, "skills", "react-best-practices");
     report += `[*] Reading rules from: ${rulesDir}\n[*] Output to: ${outputDir}\n\n`;
     try {
         const stat = await fs.stat(rulesDir);

package/commands/dev-rules.toml

@@ -3,7 +3,7 @@ description = "View development rules and coding standards"
 prompt = """
 You are a Development Standards Expert. Read and explain the development rules.
 
-@{.agent/workflows/development-rules.md}
+@{skills/workflows/development-rules.md}
 
 Based on the rules above, help the user with: {{args}}
 

package/commands/doc-rules.toml

@@ -3,7 +3,7 @@ description = "View documentation management guidelines"
 prompt = """
 You are a Documentation Manager. Read and explain the documentation guidelines.
 
-@{.agent/workflows/documentation-management.md}
+@{skills/workflows/documentation-management.md}
 
 Based on the guidelines above, help the user with: {{args}}
 

package/commands/orchestration.toml

@@ -3,7 +3,7 @@ description = "View agent orchestration protocols"
 prompt = """
 You are an Orchestration Expert. Read and explain the orchestration protocols.
 
-@{.agent/workflows/orchestration-protocol.md}
+@{skills/workflows/orchestration-protocol.md}
 
 Based on the protocols above, help the user with: {{args}}
 

package/commands/status.toml

@@ -5,7 +5,7 @@ prompt = """
 
 Loading status...
 
-{{shell ./scripts/status-dashboard.sh}}
+Call MCP `call_tool_session_manager` { command: "status" }
 
 ---
 
@@ -16,7 +16,7 @@ Loading status...
 | View specs details | `ls docs/specs/` |
 | View plans details | `ls plans/` |
 | View todos details | `ls todos/` |
-| Compound health | `./scripts/compound-dashboard.sh` |
+| Compound health | `Call MCP call_tool_compound_manager { action: "dashboard" }` |
 | Housekeeping | `/housekeeping` |
 
 What do you need to do next?

package/commands/workflow.toml

@@ -3,7 +3,7 @@ description = "View primary workflow guide (/cook)"
 prompt = """
 You are a Workflow Guide. Read and explain the primary workflow.
 
-@{.agent/workflows/primary-workflow.md}
+@{skills/workflows/primary-workflow.md}
 
 Based on the workflow above, help the user with: {{args}}
 

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "superkit-mcp-server",
-    "version": "1.2.2",
+    "version": "1.2.4",
     "type": "module",
     "description": "An MCP server for exploring and loading Super-Kit AI agent resources.",
     "main": "build/index.js",

package/skills/meta/debug/SKILL.md

@@ -34,7 +34,7 @@ Call MCP `call_tool_logger_manager` { action: "logSkill", name: "debug", outcome
 
 > **"If you haven't reproduced it, you haven't fixed it."**
 
-Always implement a reproduction case (test or script) BEFORE attempting a fix. Highly recommended to use the template at `docs/templates/repro-script-template.sh` and store artifacts in `scripts/repro/`.
+Always implement a reproduction case (test or script) BEFORE attempting a fix. Create a minimal reproduction test case that triggers the issue.
 
 > [!NOTE]
-> No top-level `debug/` folder exists. Use `skills/debug/` for guidance and `scripts/repro/` for artifacts.
+> No top-level `debug/` folder exists. Use `skills/debug/` for guidance.

package/skills/meta/debug/workflows/reproduce-issue.md

@@ -12,9 +12,9 @@ Try to strip away all unnecessary complexity.
 - Create a test case in a relevant `.test.tsx` file that mimics the user interaction.
 
 **Backend:**
-- Create a script in `scripts/repro/` that triggers the API call.
+- Create a test case or a minimal script that triggers the API call.
 
-## 3. Scripts
-Use these scripts to help:
-- `./scripts/push-env.sh` (Sync environment variables)
+## 3. Tools
+Use these to help:
 - `npm run test` (Run unit tests)
+- MCP `call_tool_compound_manager` { action: "search", terms: ["error message keywords"] } (Search for known solutions)

package/skills/meta/session-resume/SKILL.md

@@ -93,4 +93,4 @@ Consider running this skill when you see:
 - Todos: `todos/`
 - Plans: `plans/`
 - Solutions: `docs/solutions/`
-- Workflows: `.agent/workflows/`
+- Workflows: `skills/workflows/`

package/skills/tech/doc.md

@@ -18,14 +18,14 @@ Skills are folder-based packages. You can define these scopes based on your need
 
 | Scope         | Path                              | Description                          |
 | ------------- | --------------------------------- | ------------------------------------ |
-| **Workspace** | `<workspace-root>/.agent/skills/` | Available only in a specific project |
+| **Workspace** | `<workspace-root>/skills/` | Available only in a specific project |
 
 ### Skill Directory Structure
 
 ```
 my-skill/
 ├── SKILL.md      # (Required) Metadata & instructions
-├── scripts/      # (Optional) Python or Bash scripts
+├── scripts/      # (Optional) Automation scripts
 ├── references/   # (Optional) Text, documentation, templates
 └── assets/       # (Optional) Images or logos
 ```
@@ -39,7 +39,7 @@ This is an instruction-only skill; you only need to create the `SKILL.md` file.
 ### Step 1: Create the directory
 
 ```bash
-mkdir -p .agent/skills/code-review
+mkdir -p skills/code-review
 ```
 
 ### Step 2: Create SKILL.md
@@ -119,12 +119,12 @@ This skill uses a reference file in the `resources/` (or `references/`) director
 ### Step 1: Create the directory
 
 ```bash
-mkdir -p .agent/skills/license-header-adder/resources
+mkdir -p skills/license-header-adder/resources
 ```
 
 ### Step 2: Create the template file
 
-**`.agent/skills/license-header-adder/resources/HEADER.txt`**:
+**`skills/license-header-adder/resources/HEADER.txt`**:
 
 ```
 /*
@@ -136,7 +136,7 @@ mkdir -p .agent/skills/license-header-adder/resources
 
 ### Step 3: Create SKILL.md
 
-**`.agent/skills/license-header-adder/SKILL.md`**:
+**`skills/license-header-adder/SKILL.md`**:
 
 ```markdown
 ---

package/skills/workflows/compound.md

@@ -198,7 +198,7 @@ Call MCP `call_tool_todo_manager` { action: "create", priority: "p2", title: "Pr
 
 ```bash
 # Get next ID
-next_id=$(./scripts/next-todo-id.sh)
+Call MCP `call_tool_todo_manager` { action: "nextId" }
 
 # Create todo from template
 cp todos/todo-template.md todos/${next_id}-pending-p2-{description}.md

package/skills/workflows/compound_health.md

@@ -37,7 +37,7 @@ Call MCP `call_tool_compound_manager` { action: "health" }
 
 ### Step 3: Maintenance
 
-1. **Fix Orphans**: Run `./scripts/update-solution-ref.sh` on solutions you know you've used recently.
+1. **Fix Orphans**: Run `Call MCP call_tool_compound_manager { action: "updateRef" }` on solutions you know you've used recently.
 2. **Promote Patterns**: If new pattern candidates are identified, run `/compound`.
 
 ### Step 4: Record Status

package/skills/workflows/create-agent-skill.md

@@ -15,8 +15,7 @@ skills/{skill-name}/
 ├── SKILL.md        # Router + essential principles (always loaded)
 ├── workflows/      # Step-by-step procedures
 ├── references/     # Domain knowledge
-├── templates/      # Output structures
-└── scripts/        # Reusable code
+└── templates/      # Output structures
 ```
 
 ## Workflow

package/skills/workflows/generate_command.md

@@ -27,7 +27,7 @@ When to use: {trigger conditions}
 ### Step 2: Create File
 
 ```bash
-cat > .agent/workflows/{name}.md << 'EOF'
+cat > skills/workflows/{name}.md << 'EOF'
 ---
 description: {description}
 ---
@@ -65,7 +65,7 @@ EOF
 
 ```bash
 # Check file exists
-cat .agent/workflows/{name}.md
+cat skills/workflows/{name}.md
 
 # Test invocation
 /{name}

package/skills/workflows/housekeeping.md

@@ -127,7 +127,7 @@ Check if any deprecated ADRs need review (haven't been reviewed in 6+ months):
 
 ```bash
 // turbo
-./scripts/check-deprecated-adrs.sh
+Call MCP `call_tool_compound_manager` { action: "validate" }
 ```
 
 - If warnings appear, review the deprecated ADR to see if it can be archived or needs an update.
@@ -140,7 +140,7 @@ Prevent log files from growing indefinitely:
 ```bash
 # Rotate logs older than 12 weeks
 // turbo
-./scripts/rotate-logs.sh
+Call MCP `call_tool_logger_manager` { action: "rotateLogs" }
 ```
 
 ### Step 3.8: Documentation Freshness Check
@@ -155,7 +155,7 @@ Call MCP `call_tool_docs_manager` { action: "freshness" }
 **The script checks:**
 - [ ] Files changed in last commit have corresponding doc updates
 - [ ] New scripts are mentioned in README files
-- [ ] New workflows are indexed in `.agent/workflows/README.md`
+- [ ] New workflows are indexed in `skills/workflows/README.md`
 
 **If warnings appear:** Update docs before pushing.
 

package/skills/workflows/plan-compound.md

@@ -53,9 +53,9 @@ Copy the **table** AND the **update command** from the script output into your p
 
 Before proceeding to Step 0.5, confirm:
 
-- [ ] Ran `compound-search.sh` with relevant keywords?
+- [ ] Ran MCP `call_tool_compound_manager` { action: "search" } with relevant keywords?
 - [ ] Reviewed all matching solutions (or confirmed none found)?
-- [ ] Ran `update-solution-ref.sh` if reusing any solution?
+- [ ] Ran MCP `call_tool_compound_manager` { action: "updateRef" } if reusing any solution?
 
 **If any box is unchecked:** Complete it now. Do NOT proceed.
 

package/skills/workflows/skill-review.md

@@ -33,12 +33,12 @@ Call MCP `call_tool_logger_manager` { action: "logSkill", name: "compound-docs",
 
 1. **Check suggestion volume:**
    ```bash
-   wc -l .agent/logs/skill_suggestions.csv
+   wc -l docs/agents/logs/skill_suggestions.csv
    ```
 
 2. **View unique suggestions:**
    ```bash
-   cut -d',' -f1 .agent/logs/skill_suggestions.csv | sort | uniq -c | sort -nr | head -20
+   cut -d',' -f1 docs/agents/logs/skill_suggestions.csv | sort | uniq -c | sort -nr | head -20
    ```
 
 3. **Identify candidates:**
@@ -78,7 +78,7 @@ If a clear gap exists:
 If it's a synonym for an existing skill:
 
 1. Add keywords to the existing `SKILL.md` description
-2. Update `.agent/workflows/README.md` to reference it
+2. Update `skills/workflows/README.md` to reference it
 
 #### Option C: Archive (Low Value)
 If it's noise or one-off:
@@ -95,10 +95,10 @@ If it's noise or one-off:
 
 ```bash
 # Append to archive
-cat .agent/logs/skill_suggestions.csv >> .agent/logs/skill_suggestions_archive.csv
+cat docs/agents/logs/skill_suggestions.csv >> docs/agents/logs/skill_suggestions_archive.csv
 
 # Clear active log
-printf "suggestion,context,count\n" > .agent/logs/skill_suggestions.csv
+printf "suggestion,context,count\n" > docs/agents/logs/skill_suggestions.csv
 ```
 
 ---

package/skills/workflows/triage-sprint.md

@@ -12,7 +12,7 @@ Rapidly process pending work items with strict time-boxing to clear backlog bott
 
 - When "Pending Todos" count > 20
 - Weekly (Fridays) to clear the deck
-- When `compound-dashboard.sh` shows "Bottleneck" warning
+- When MCP `call_tool_compound_manager` { action: "dashboard" } shows "Bottleneck" warning
 
 ---
 

package/skills/workflows/work.md

@@ -233,8 +233,8 @@ Call MCP `call_tool_todo_manager` { action: "create", priority: "p2", title: "{d
 **Common docs to update:**
 | Change Type | Update Target |
 |-------------|---------------|
-| New script | Add to relevant README (e.g., `scripts/README.md`) |
-| New workflow | Add to `.agent/workflows/README.md` |
+| New MCP tool | Update relevant README |
+| New workflow | Add to `skills/workflows/README.md` |
 | New API endpoint | Update API documentation |
 | New component | Update component docs |
 | Config change | Update setup/installation docs |