agent-enderun 1.1.0 → 1.1.2

package/agent.md

@@ -2,24 +2,24 @@
 
 This is the primary entry point when using Agent Enderun within the Antigravity (IDE & CLI) ecosystem.
 
-The framework operates under a unified governance structure located in the .enderun/ directory.
+The framework operates under a unified governance structure located in the .agent/ directory.
 
 ### Primary Constitution
 All governance rules, agent checklists, and project memory live here:
 
-👉 **[.enderun/ENDERUN.md](.enderun/ENDERUN.md)**
+👉 **[.agent/ENDERUN.md](.agent/ENDERUN.md)**
 
 ### 🤖 Agent Directive
 You are operating under the Agent Enderun governance framework.
 
 At the **start of every session**, before any work:
-1. **Restore Memory:** Read `.enderun/PROJECT_MEMORY.md` to restore state, active Trace ID, and history.
-2. **Load Identity:** Read the relevant agent definition under `.enderun/agents/{agent}.json` (default to `@manager`).
-3. **Internalize Knowledge:** Reference the `.enderun/knowledge/` base for architectural and coding standards.
+1. **Restore Memory:** Read `.agent/PROJECT_MEMORY.md` to restore state, active Trace ID, and history.
+2. **Load Identity:** Read the relevant agent definition under `.agent/skills/{agent}.json` (default to `@manager`).
+3. **Internalize Knowledge:** Reference the `.agent/rules/` base for architectural and coding standards.
 
 ### 🛡️ Core Mandates
 - **Surgical Edits:** Use `replace_text` or `patch_file` via MCP for precise changes.
 - **Traceability:** Every action must inherit the active Trace ID from memory.
 - **Contract First:** No implementation without verified types.
 
-All paths and references inside the project must comply with the Supreme Constitution located at `.enderun/ENDERUN.md`.
+All paths and references inside the project must comply with the Supreme Constitution located at `.agent/ENDERUN.md`.

package/bin/cli.js

@@ -6,11 +6,10 @@ import { dirname, join } from "node:path";
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = dirname(__filename);
 
-const cliPath = join(__dirname, "../src/cli/index.ts");
+const cliPath = join(__dirname, "../dist/src/cli/index.js");
 
-// use shell: false to prevent argument (quote) corruption
-const cmd = process.platform === "win32" ? "npx.cmd" : "npx";
-const child = spawn(cmd, ["tsx", cliPath, ...process.argv.slice(2)], {
+const cmd = "node";
+const child = spawn(cmd, [cliPath, ...process.argv.slice(2)], {
     stdio: "inherit",
     shell: false 
 });

package/bin/compile.js

@@ -0,0 +1,22 @@
+import ts from 'typescript';
+import fs from 'fs';
+import path from 'path';
+
+const configJson = JSON.parse(fs.readFileSync('tsconfig.json', 'utf8'));
+const parsedConfig = ts.parseJsonConfigFileContent(configJson, ts.sys, '.');
+const program = ts.createProgram(parsedConfig.fileNames, parsedConfig.options);
+const emitResult = program.emit();
+
+const allDiagnostics = ts
+  .getPreEmitDiagnostics(program)
+  .concat(emitResult.diagnostics);
+
+allDiagnostics.forEach(diagnostic => {
+  if (diagnostic.file) {
+    let { line, character } = ts.getLineAndCharacterOfPosition(diagnostic.file, diagnostic.start);
+    let message = ts.flattenDiagnosticMessageText(diagnostic.messageText, '\n');
+    console.log(`${diagnostic.file.fileName} (${line + 1},${character + 1}): ${message}`);
+  } else {
+    console.log(ts.flattenDiagnosticMessageText(diagnostic.messageText, '\n'));
+  }
+});

package/bin/test-init-run.js

@@ -0,0 +1,136 @@
+import fs from 'fs';
+import path from 'path';
+import { initCommand } from '../dist/src/cli/commands/init.js';
+
+const adapters = [
+    { id: "gemini", dir: ".enderun", shim: "GEMINI.md" },
+    { id: "claude", dir: ".enderun", shim: "CLAUDE.md" },
+    { id: "cursor", dir: ".enderun", shim: ".cursor/rules/global.mdc" },
+    { id: "codex", dir: ".enderun", shim: ".github/copilot-instructions.md" },
+    { id: "grok", dir: ".enderun", shim: "GROK.md" },
+    { id: "antigravity", dir: ".enderun", shim: "agent.md" },
+    { id: "antigravity-cli", dir: ".enderun", shim: "agent.md" }
+];
+
+const projectRoot = process.cwd();
+const testBase = path.join(projectRoot, "dist", "init-adapters");
+
+// Redirect HOME to a mock directory inside the permitted workspace
+const mockHome = path.join(testBase, "mock-home");
+process.env.HOME = mockHome;
+process.env.USERPROFILE = mockHome;
+
+// Pre-create the directory structure and file for Claude Desktop config so the post-init step successfully runs
+const claudeConfigDir = path.join(mockHome, "Library", "Application Support", "Claude");
+fs.mkdirSync(claudeConfigDir, { recursive: true });
+fs.writeFileSync(path.join(claudeConfigDir, "claude_desktop_config.json"), JSON.stringify({ mcpServers: {} }));
+
+console.log("🚀 Starting Realistic Programmatic Validation of Adapter Init Commands...");
+
+let failed = 0;
+
+for (const adapter of adapters) {
+    console.log(`\n--------------------------------------------`);
+    console.log(`🧪 Testing Adapter: ${adapter.id}`);
+    
+    const targetDir = path.join(testBase, adapter.id);
+    if (!fs.existsSync(targetDir)) {
+        fs.mkdirSync(targetDir, { recursive: true });
+    }
+    // Write a mock package.json to act as project root
+    const mockPkgPath = path.join(targetDir, "package.json");
+    if (!fs.existsSync(mockPkgPath)) {
+        fs.writeFileSync(mockPkgPath, JSON.stringify({
+            name: `mock-project-${adapter.id}`,
+            version: "1.0.0",
+            type: "module"
+        }, null, 2));
+    }
+    // Pre-create .git directory to prevent initCommand from invoking 'git init' (which is blocked by the sandbox)
+    const mockGitDir = path.join(targetDir, ".git");
+    if (!fs.existsSync(mockGitDir)) {
+        fs.mkdirSync(mockGitDir, { recursive: true });
+    }
+
+    try {
+        // Change process CWD to target directory to simulate running init there
+        process.chdir(targetDir);
+        
+        // Temporarily bypass the CLI check and validations in init.ts (which would try to run validate-agent-army)
+        process.env.ENDERUN_SKIP_INSTALL = "1";
+        
+        // Execute the initCommand programmatically
+        await initCommand(adapter.id, false);
+        
+        // Restore CWD
+        process.chdir(projectRoot);
+
+        // 1. Check framework directory
+        const frameworkPath = path.join(targetDir, adapter.dir);
+        if (fs.existsSync(frameworkPath)) {
+            console.log(`✅ Framework directory created: ${adapter.dir}`);
+        } else {
+            console.log(`❌ Framework directory MISSING: ${adapter.dir}`);
+            failed++;
+            continue;
+        }
+
+        // 2. Check shim file
+        const shimPath = path.join(targetDir, adapter.shim);
+        if (fs.existsSync(shimPath)) {
+            console.log(`✅ Shim file created: ${adapter.shim}`);
+        } else {
+            console.log(`❌ Shim file MISSING: ${adapter.shim}`);
+            failed++;
+            continue;
+        }
+
+        // 3. Check memory initialization
+        const memoryPath = fs.existsSync(path.join(frameworkPath, "memory/PROJECT_MEMORY.md"))
+            ? path.join(frameworkPath, "memory/PROJECT_MEMORY.md")
+            : path.join(frameworkPath, "PROJECT_MEMORY.md");
+            
+        if (fs.existsSync(memoryPath)) {
+            console.log(`✅ PROJECT_MEMORY.md created successfully.`);
+        } else {
+            console.log(`❌ PROJECT_MEMORY.md is MISSING!`);
+            failed++;
+            continue;
+        }
+
+        // 4. Check agents folder
+        let agentFolder = "agents";
+        if (adapter.id === "antigravity") {
+            agentFolder = "skills";
+        } else if (adapter.id === "grok") {
+            agentFolder = "plugins";
+        }
+        const agentsPath = path.join(frameworkPath, agentFolder);
+        if (fs.existsSync(agentsPath)) {
+            const files = fs.readdirSync(agentsPath);
+            const agentCount = files.filter(f => f.endsWith(".json")).length;
+            console.log(`✅ Agent configurations created: ${agentsPath} (${agentCount} agents found)`);
+            if (agentCount === 0) {
+                console.log(`❌ No agent configuration files found in folder!`);
+                failed++;
+            }
+        } else {
+            console.log(`❌ Agents directory MISSING: ${agentsPath}`);
+            failed++;
+        }
+
+    } catch (error) {
+        // Ensure CWD is restored in case of error
+        process.chdir(projectRoot);
+        console.error(`❌ Init failed with error:`, error.message);
+        failed++;
+    }
+}
+
+console.log(`\n--------------------------------------------`);
+if (failed > 0) {
+    console.error(`❌ Validation FAILED. ${failed} checks failed.`);
+    process.exit(1);
+} else {
+    console.log(`🎉 SUCCESS! All ${adapters.length} adapters initialized programmatically and passed checks.`);
+}

package/dist/framework-mcp/src/index.js

@@ -5,7 +5,7 @@ import { TOOLS, toolHandlers } from "./tools/index.js";
 // ─── Server Setup ─────────────────────────────────────────────────
 const server = new Server({
     name: "@agent-enderun/mcp",
-    version: "1.0.9",
+    version: "1.1.2",
 }, {
     capabilities: {
         tools: {},

package/dist/framework-mcp/src/tools/definitions.js

@@ -1,11 +1,13 @@
 export const TOOLS = [
     {
         name: "read_file",
-        description: "Read the content of a file within the project.",
+        description: "Read the content of a file within the project. Supports optional line range reading to prevent stream overload.",
         inputSchema: {
             type: "object",
             properties: {
                 path: { type: "string", description: "Path to the file relative to project root" },
+                startLine: { type: "number", description: "Optional starting line number (1-indexed)" },
+                endLine: { type: "number", description: "Optional ending line number (inclusive)" },
             },
             required: ["path"],
         },

package/dist/framework-mcp/src/tools/definitions.js.map

@@ -1 +1 @@
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+{"version":3,"file":"definitions.js","sourceRoot":"","sources":["../../../../framework-mcp/src/tools/definitions.ts"],"names":[],"mappings":"AAEA,MAAM,CAAC,MAAM,KAAK,GAAqB;IACnC;QACI,IAAI,EAAE,WAAW;QACjB,WAAW,EAAE,iHAAiH;QAC9H,WAAW,EAAE;YACT,IAAI,EAAE,QAAQ;YACd,UAAU,EAAE;gBACR,IAAI,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,2CAA2C,EAAE;gBAClF,SAAS,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,2CAA2C,EAAE;gBACvF,OAAO,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,yCAAyC,EAAE;aACtF;YACD,QAAQ,EAAE,CAAC,MAAM,CAAC;SACrB;KACJ;IACD;QACI,IAAI,EAAE,YAAY;QAClB,WAAW,EAAE,0DAA0D;QACvE,WAAW,EAAE;YACT,IAAI,EAAE,QAAQ;YACd,UAAU,EAAE;gBACR,IAAI,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,2CAA2C,EAAE;gBAClF,OAAO,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,8BAA8B,EAAE;aAC3E;YACD,QAAQ,EAAE,CAAC,MAAM,EAAE,SAAS,CAAC;SAChC;KACJ;IACD;QACI,IAAI,EAAE,cAAc;QACpB,WAAW,EAAE,4DAA4D;QACzE,WAAW,EAAE;YACT,IAAI,EAAE,QAAQ;YACd,UAAU,EAAE;gBACR,IAAI,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,kBAAkB,EAAE;gBACzD,OAAO,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,wBAAwB,EAAE;gBAClE,OAAO,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,6BAA6B,EAAE;aAC1E;YACD,QAAQ,EAAE,CAAC,MAAM,EAAE,SAAS,EAAE,SAAS,CAAC;SAC3C;KACJ;IACD;QACI,IAAI,EAAE,YAAY;QAClB,WAAW,EAAE,2EAA2E;QACxF,WAAW,EAAE;YACT,IAAI,EAAE,QAAQ;YACd,UAAU,EAAE;gBACR,IAAI,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,kBAAkB,EAAE;gBACzD,SAAS,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,kCAAkC,EAAE;gBAC9E,OAAO,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,gCAAgC,EAAE;gBAC1E,UAAU,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,yBAAyB,EAAE;aACzE;YACD,QAAQ,EAAE,CAAC,MAAM,EAAE,WAAW,EAAE,SAAS,EAAE,YAAY,CAAC;SAC3D;KACJ;IACD;QACI,IAAI,EAAE,sBAAsB;QAC5B,WAAW,EAAE,iEAAiE;QAC9E,WAAW,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,UAAU,EAAE,EAAE,EAAE;KAClD;IACD;QACI,IAAI,EAAE,uBAAuB;QAC7B,WAAW,EAAE,iDAAiD;QAC9D,WAAW,EAAE;YACT,IAAI,EAAE,QAAQ;YACd,UAAU,EAAE;gBACR,OAAO,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,4CAA4C,EAAE;gBACtF,OAAO,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,mCAAmC,EAAE;aAChF;YACD,QAAQ,EAAE,CAAC,SAAS,EAAE,SAAS,CAAC;SACnC;KACJ;IACD;QACI,IAAI,EAAE,kBAAkB;QACxB,WAAW,EAAE,4EAA4E;QACzF,WAAW,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,UAAU,EAAE,EAAE,EAAE;KAClD;IACD;QACI,IAAI,EAAE,oBAAoB;QAC1B,WAAW,EAAE,kDAAkD;QAC/D,WAAW,EAAE;YACT,IAAI,EAAE,QAAQ;YACd,UAAU,EAAE;gBACR,IAAI,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,uEAAuE,EAAE;gBAC9G,EAAE,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,oCAAoC,EAAE;gBACzE,QAAQ,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,IAAI,EAAE,CAAC,QAAQ,EAAE,YAAY,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE;gBAC7E,OAAO,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,iBAAiB,EAAE;gBAC3D,OAAO,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,iBAAiB,EAAE;aAC9D;YACD,QAAQ,EAAE,CAAC,IAAI,EAAE,UAAU,EAAE,SAAS,EAAE,SAAS,CAAC;SACrD;KACJ;IACD;QACI,IAAI,EAAE,kBAAkB;QACxB,WAAW,EAAE,4CAA4C;QACzD,WAAW,EAAE;YACT,IAAI,EAAE,QAAQ;YACd,UAAU,EAAE;gBACR,KAAK,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,2CAA2C,EAAE;gBACnF,MAAM,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,qBAAqB,EAAE;gBAC9D,OAAO,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,qBAAqB,EAAE;gBAC/D,MAAM,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,IAAI,EAAE,CAAC,SAAS,EAAE,SAAS,CAAC,EAAE,WAAW,EAAE,0BAA0B,EAAE;gBACjG,OAAO,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,uCAAuC,EAAE;gBACjF,QAAQ,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,8CAA8C,EAAE;aAC5F;YACD,QAAQ,EAAE,CAAC,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAE,QAAQ,EAAE,SAAS,CAAC;SAChE;KACJ;IACD;QACI,IAAI,EAAE,sBAAsB;QAC5B,WAAW,EAAE,gEAAgE;QAC7E,WAAW,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,UAAU,EAAE,EAAE,EAAE;KAClD;CACJ,CAAC"}

package/dist/framework-mcp/src/tools/file_system/read_file.js

@@ -2,7 +2,27 @@ import fs from "fs";
 import { safePath } from "../../utils/security.js";
 export function handleReadFile(projectRoot, args) {
     const filePath = safePath(projectRoot, args.path);
+    const startLine = args.startLine !== undefined ? Number(args.startLine) : undefined;
+    const endLine = args.endLine !== undefined ? Number(args.endLine) : undefined;
     const content = fs.readFileSync(filePath, "utf8");
+    const lines = content.split(/\r?\n/);
+    if (startLine !== undefined || endLine !== undefined) {
+        const start = startLine !== undefined ? Math.max(1, startLine) - 1 : 0;
+        const end = endLine !== undefined ? Math.min(lines.length, endLine) : lines.length;
+        const sliced = lines.slice(start, end).join("\n");
+        return { content: [{ type: "text", text: sliced }] };
+    }
+    // Default protection limit: 1000 lines
+    const DEFAULT_MAX_LINES = 1000;
+    if (lines.length > DEFAULT_MAX_LINES) {
+        const sliced = lines.slice(0, DEFAULT_MAX_LINES).join("\n");
+        return {
+            content: [{
+                    type: "text",
+                    text: `${sliced}\n\n... [TRUNCATED - File is too long (${lines.length} lines). Only the first ${DEFAULT_MAX_LINES} lines are shown. Use startLine and endLine parameters to read other parts of the file.]`
+                }]
+        };
+    }
     return { content: [{ type: "text", text: content }] };
 }
 //# sourceMappingURL=read_file.js.map

package/dist/framework-mcp/src/tools/file_system/read_file.js.map

@@ -1 +1 @@
-{"version":3,"file":"read_file.js","sourceRoot":"","sources":["../../../../../framework-mcp/src/tools/file_system/read_file.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,IAAI,CAAC;AACpB,OAAO,EAAE,QAAQ,EAAE,MAAM,yBAAyB,CAAC;AAGnD,MAAM,UAAU,cAAc,CAAC,WAAmB,EAAE,IAAc;IAC9D,MAAM,QAAQ,GAAG,QAAQ,CAAC,WAAW,EAAE,IAAI,CAAC,IAAc,CAAC,CAAC;IAC5D,MAAM,OAAO,GAAG,EAAE,CAAC,YAAY,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC;IAClD,OAAO,EAAE,OAAO,EAAE,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,CAAC,EAAE,CAAC;AAC1D,CAAC"}
+{"version":3,"file":"read_file.js","sourceRoot":"","sources":["../../../../../framework-mcp/src/tools/file_system/read_file.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,IAAI,CAAC;AACpB,OAAO,EAAE,QAAQ,EAAE,MAAM,yBAAyB,CAAC;AAGnD,MAAM,UAAU,cAAc,CAAC,WAAmB,EAAE,IAAc;IAC9D,MAAM,QAAQ,GAAG,QAAQ,CAAC,WAAW,EAAE,IAAI,CAAC,IAAc,CAAC,CAAC;IAC5D,MAAM,SAAS,GAAG,IAAI,CAAC,SAAS,KAAK,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC;IACpF,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,KAAK,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC;IAE9E,MAAM,OAAO,GAAG,EAAE,CAAC,YAAY,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC;IAClD,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;IAErC,IAAI,SAAS,KAAK,SAAS,IAAI,OAAO,KAAK,SAAS,EAAE,CAAC;QACnD,MAAM,KAAK,GAAG,SAAS,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QACvE,MAAM,GAAG,GAAG,OAAO,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC;QACnF,MAAM,MAAM,GAAG,KAAK,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QAClD,OAAO,EAAE,OAAO,EAAE,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC;IACzD,CAAC;IAED,uCAAuC;IACvC,MAAM,iBAAiB,GAAG,IAAI,CAAC;IAC/B,IAAI,KAAK,CAAC,MAAM,GAAG,iBAAiB,EAAE,CAAC;QACnC,MAAM,MAAM,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,iBAAiB,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QAC5D,OAAO;YACH,OAAO,EAAE,CAAC;oBACN,IAAI,EAAE,MAAM;oBACZ,IAAI,EAAE,GAAG,MAAM,0CAA0C,KAAK,CAAC,MAAM,2BAA2B,iBAAiB,0FAA0F;iBAC9M,CAAC;SACL,CAAC;IACN,CAAC;IAED,OAAO,EAAE,OAAO,EAAE,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,CAAC,EAAE,CAAC;AAC1D,CAAC"}

package/dist/framework-mcp/src/tools/messaging/send_message.js

@@ -3,22 +3,45 @@ import path from "path";
 import { resolveFrameworkDir } from "../../utils/security.js";
 export function handleSendAgentMessage(projectRoot, args) {
     const { to, category, content, traceId } = args;
-    // `from` is optional — falls back to "@mcp" for backward compatibility
     const from = args.from || "@mcp";
     const frameworkDir = resolveFrameworkDir(projectRoot);
+    const messagesDir = path.join(projectRoot, frameworkDir, "messages");
     const agentName = to.replace("@", "");
-    const messagePath = path.join(projectRoot, frameworkDir, "messages", `${agentName}.json`);
-    const message = {
-        timestamp: new Date().toISOString(),
-        from,
-        to,
-        category,
-        traceId,
-        content,
-        status: "PENDING"
-    };
-    fs.mkdirSync(path.dirname(messagePath), { recursive: true });
-    fs.appendFileSync(messagePath, JSON.stringify(message) + "\n");
-    return { content: [{ type: "text", text: `✅ Message sent to ${to} (from: ${from})` }] };
+    const messagePath = path.join(messagesDir, `${agentName}.json`);
+    const lockPath = path.join(messagesDir, ".lock");
+    // Hermes Lock Protocol: Retry 3 times with 500ms delay
+    let retries = 3;
+    while (retries > 0 && fs.existsSync(lockPath)) {
+        const stats = fs.statSync(lockPath);
+        if (Date.now() - stats.mtimeMs > 5000) {
+            fs.unlinkSync(lockPath);
+            break;
+        }
+        retries--;
+        if (retries > 0) {
+            const start = Date.now();
+            while (Date.now() - start < 500)
+                ; // Simple busy wait for MCP environment
+        }
+    }
+    try {
+        fs.mkdirSync(messagesDir, { recursive: true });
+        fs.writeFileSync(lockPath, `Locked by ${from} at ${new Date().toISOString()}`);
+        const message = {
+            timestamp: new Date().toISOString(),
+            from,
+            to,
+            category,
+            traceId,
+            content,
+            status: "PENDING"
+        };
+        fs.appendFileSync(messagePath, JSON.stringify(message) + "\n");
+        return { content: [{ type: "text", text: `✅ Message sent to ${to} (from: ${from})` }] };
+    }
+    finally {
+        if (fs.existsSync(lockPath))
+            fs.unlinkSync(lockPath);
+    }
 }
 //# sourceMappingURL=send_message.js.map

package/dist/framework-mcp/src/tools/messaging/send_message.js.map

@@ -1 +1 @@
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+{"version":3,"file":"send_message.js","sourceRoot":"","sources":["../../../../../framework-mcp/src/tools/messaging/send_message.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,IAAI,CAAC;AACpB,OAAO,IAAI,MAAM,MAAM,CAAC;AACxB,OAAO,EAAE,mBAAmB,EAAE,MAAM,yBAAyB,CAAC;AAG9D,MAAM,UAAU,sBAAsB,CAAC,WAAmB,EAAE,IAAc;IACtE,MAAM,EAAE,EAAE,EAAE,QAAQ,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,IAA2E,CAAC;IACvH,MAAM,IAAI,GAAI,IAAI,CAAC,IAAe,IAAI,MAAM,CAAC;IAE7C,MAAM,YAAY,GAAG,mBAAmB,CAAC,WAAW,CAAC,CAAC;IACtD,MAAM,WAAW,GAAG,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE,YAAY,EAAE,UAAU,CAAC,CAAC;IACrE,MAAM,SAAS,GAAG,EAAE,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC;IACtC,MAAM,WAAW,GAAG,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE,GAAG,SAAS,OAAO,CAAC,CAAC;IAChE,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE,OAAO,CAAC,CAAC;IAEjD,uDAAuD;IACvD,IAAI,OAAO,GAAG,CAAC,CAAC;IAChB,OAAO,OAAO,GAAG,CAAC,IAAI,EAAE,CAAC,UAAU,CAAC,QAAQ,CAAC,EAAE,CAAC;QAC5C,MAAM,KAAK,GAAG,EAAE,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC;QACpC,IAAI,IAAI,CAAC,GAAG,EAAE,GAAG,KAAK,CAAC,OAAO,GAAG,IAAI,EAAE,CAAC;YACpC,EAAE,CAAC,UAAU,CAAC,QAAQ,CAAC,CAAC;YACxB,MAAM;QACV,CAAC;QACD,OAAO,EAAE,CAAC;QACV,IAAI,OAAO,GAAG,CAAC,EAAE,CAAC;YACd,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;YACzB,OAAO,IAAI,CAAC,GAAG,EAAE,GAAG,KAAK,GAAG,GAAG;gBAAC,CAAC,CAAC,uCAAuC;QAC7E,CAAC;IACL,CAAC;IAED,IAAI,CAAC;QACD,EAAE,CAAC,SAAS,CAAC,WAAW,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;QAC/C,EAAE,CAAC,aAAa,CAAC,QAAQ,EAAE,aAAa,IAAI,OAAO,IAAI,IAAI,EAAE,CAAC,WAAW,EAAE,EAAE,CAAC,CAAC;QAE/E,MAAM,OAAO,GAAG;YACZ,SAAS,EAAE,IAAI,IAAI,EAAE,CAAC,WAAW,EAAE;YACnC,IAAI;YACJ,EAAE;YACF,QAAQ;YACR,OAAO;YACP,OAAO;YACP,MAAM,EAAE,SAAS;SACpB,CAAC;QAEF,EAAE,CAAC,cAAc,CAAC,WAAW,EAAE,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,GAAG,IAAI,CAAC,CAAC;QAC/D,OAAO,EAAE,OAAO,EAAE,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,qBAAqB,EAAE,WAAW,IAAI,GAAG,EAAE,CAAC,EAAE,CAAC;IAC5F,CAAC;YAAS,CAAC;QACP,IAAI,EAAE,CAAC,UAAU,CAAC,QAAQ,CAAC;YAAE,EAAE,CAAC,UAAU,CAAC,QAAQ,CAAC,CAAC;IACzD,CAAC;AACL,CAAC"}

package/dist/src/cli/adapters.d.ts

@@ -24,7 +24,9 @@ export declare function remapFrameworkContent(content: string, frameworkDir: str
 export declare function buildMcpServerEntry(projectRoot: string): {
     command: string;
     args: string[];
-    env: {};
+    env: {
+        ENDERUN_PROJECT_ROOT: string;
+    };
 };
 /**
  * Adapter-specific MCP and IDE hooks after scaffold.

package/dist/src/cli/adapters.js

@@ -6,14 +6,14 @@ export const ADAPTER_IDS = ["gemini", "claude", "grok", "cursor", "codex", "anti
 export const ADAPTERS = {
     gemini: {
         id: "gemini",
-        frameworkDir: ".gemini",
-        shimFile: "gemini.md",
+        frameworkDir: ".enderun",
+        shimFile: "GEMINI.md",
         templateDir: ".enderun",
         nestedDirs: ["agents", "skills", "knowledge"],
     },
     claude: {
         id: "claude",
-        frameworkDir: ".claude",
+        frameworkDir: ".enderun",
         shimFile: "CLAUDE.md",
         templateDir: ".enderun",
         nestedDirs: ["agents", "skills", "knowledge"],
@@ -34,24 +34,24 @@ export const ADAPTERS = {
     },
     grok: {
         id: "grok",
-        frameworkDir: ".grok",
-        shimFile: "grok.md",
+        frameworkDir: ".enderun",
+        shimFile: "GROK.md",
         templateDir: ".enderun",
-        nestedDirs: ["plugins", "agents", "knowledge"],
+        nestedDirs: ["agents", "skills", "knowledge"],
     },
     antigravity: {
         id: "antigravity",
-        frameworkDir: ".agent",
+        frameworkDir: ".enderun",
         shimFile: "agent.md",
         templateDir: ".enderun",
-        nestedDirs: ["skills", "workflows", "rules", "knowledge"],
+        nestedDirs: ["agents", "skills", "knowledge"],
     },
     "antigravity-cli": {
         id: "antigravity-cli",
-        frameworkDir: ".gemini/antigravity-cli",
+        frameworkDir: ".enderun",
         shimFile: "agent.md",
         templateDir: ".enderun",
-        nestedDirs: ["agents", "skills"],
+        nestedDirs: ["agents", "skills", "knowledge"],
     },
 };
 /**
@@ -181,7 +181,9 @@ export function buildMcpServerEntry(projectRoot) {
     return {
         command: "node",
         args: [path.join(projectRoot, "framework-mcp/dist/index.js")],
-        env: {},
+        env: {
+            ENDERUN_PROJECT_ROOT: projectRoot,
+        },
     };
 }
 function writeAntigravityScaffold(frameworkDirPath) {

package/dist/src/cli/adapters.js.map

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package/dist/src/cli/commands/check.js

@@ -33,7 +33,6 @@ export function checkCommand() {
         { name: "MCP Config (mcp.json)", path: "mcp.json" },
         { name: "ESLint Config (eslint.config.js)", path: "eslint.config.js" },
         { name: "ESLint Standards", path: path.join(frameworkDir, `${knowledgeDir}/eslint-standards.md`) },
-        { name: "Backend Contract", path: path.join(pathsMap.backend, "contract.version.json") },
         { name: "MCP Server", path: "framework-mcp/package.json" },
         { name: "Panda CSS Config", path: "panda.config.ts" },
         { name: "Brain Dashboard", path: path.join(frameworkDir, "BRAIN_DASHBOARD.md") },
@@ -43,6 +42,10 @@ export function checkCommand() {
         { name: "Professional Error Handling Pattern", path: path.join(pathsMap.docs, "backend/error-handling.md") },
         { name: "Atomic Component Standards", path: path.join(pathsMap.docs, "frontend/component-patterns.md") },
     ];
+    // Optional app-level checks (only when apps/ has content)
+    const optionalChecks = [
+        { name: "Backend Contract", path: path.join(pathsMap.backend, "contract.version.json") },
+    ];
     for (const check of checks) {
         if (fs.existsSync(path.join(process.cwd(), check.path))) {
             console.warn(`✅ ${check.name} found.`);
@@ -52,6 +55,14 @@ export function checkCommand() {
             issues++;
         }
     }
+    for (const check of optionalChecks) {
+        if (fs.existsSync(path.join(process.cwd(), check.path))) {
+            console.warn(`✅ ${check.name} found.`);
+        }
+        else {
+            console.warn(`ℹ️  ${check.name} not found (${check.path}) — created with 'create-app'.`);
+        }
+    }
     // Dependency Check
     const mcpNodeModules = path.join(process.cwd(), "framework-mcp/node_modules");
     const rootNodeModules = path.join(process.cwd(), "node_modules");

package/dist/src/cli/commands/check.js.map

@@ -1 +1 @@
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+{"version":3,"file":"check.js","sourceRoot":"","sources":["../../../../src/cli/commands/check.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,IAAI,CAAC;AACpB,OAAO,IAAI,MAAM,MAAM,CAAC;AACxB,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAC;AAEzC,OAAO,EAAE,eAAe,EAAE,kBAAkB,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAC;AACxF,OAAO,EAAE,iBAAiB,EAAE,gBAAgB,EAAE,MAAM,iBAAiB,CAAC,CAAC,2EAA2E;AAElJ,MAAM,iBAAiB,GAAG,iBAAiB,EAAE,CAAC;AAE9C;;;;GAIG;AACH,MAAM,UAAU,YAAY;IACxB,OAAO,CAAC,IAAI,CAAC,sCAAsC,iBAAiB,MAAM,CAAC,CAAC;IAC5E,IAAI,MAAM,GAAG,CAAC,CAAC;IAEf,MAAM,YAAY,GAAG,eAAe,EAAE,CAAC;IACvC,MAAM,QAAQ,GAAG,kBAAkB,EAAE,CAAC;IACtC,MAAM,UAAU,GAAG,aAAa,EAAE,CAAC;IAEnC,OAAO,CAAC,IAAI,CAAC,2BAA2B,YAAY,2BAA2B,CAAC,CAAC;IAEjF,iFAAiF;IACjF,IAAI,YAAY,GAAG,WAAW,CAAC;IAC/B,IAAI,YAAY,KAAK,SAAS,IAAI,YAAY,KAAK,QAAQ,EAAE,CAAC;QAC1D,YAAY,GAAG,OAAO,CAAC;IAC3B,CAAC;IAED,MAAM,gBAAgB,GAAG,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,YAAY,CAAC,CAAC;QAC1E,CAAC,CAAC,YAAY;QACd,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,YAAY,CAAC,CAAC;IAE5C,MAAM,MAAM,GAAG;QACX,EAAE,IAAI,EAAE,2BAA2B,EAAE,IAAI,EAAE,gBAAgB,EAAE;QAC7D,EAAE,IAAI,EAAE,4BAA4B,EAAE,IAAI,EAAE,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,UAAU,CAAC,EAAE;QACtF,EAAE,IAAI,EAAE,iCAAiC,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,mBAAmB,CAAC,EAAE;QAC/F,EAAE,IAAI,EAAE,gCAAgC,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,aAAa,CAAC,EAAE;QACxF,EAAE,IAAI,EAAE,0BAA0B,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,WAAW,CAAC,EAAE;QAChF,EAAE,IAAI,EAAE,uBAAuB,EAAE,IAAI,EAAE,UAAU,EAAE;QACnD,EAAE,IAAI,EAAE,kCAAkC,EAAE,IAAI,EAAE,kBAAkB,EAAE;QACtE,EAAE,IAAI,EAAE,kBAAkB,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,GAAG,YAAY,sBAAsB,CAAC,EAAE;QAClG,EAAE,IAAI,EAAE,YAAY,EAAE,IAAI,EAAE,4BAA4B,EAAE;QAC1D,EAAE,IAAI,EAAE,kBAAkB,EAAE,IAAI,EAAE,iBAAiB,EAAE;QACrD,EAAE,IAAI,EAAE,iBAAiB,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,oBAAoB,CAAC,EAAE;QAChF,EAAE,IAAI,EAAE,+CAA+C,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,EAAE,WAAW,CAAC,EAAE;QACtG,EAAE,IAAI,EAAE,wDAAwD,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,EAAE,oBAAoB,CAAC,EAAE;QACxH,EAAE,IAAI,EAAE,oCAAoC,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,EAAE,gCAAgC,CAAC,EAAE;QAChH,EAAE,IAAI,EAAE,qCAAqC,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,EAAE,2BAA2B,CAAC,EAAE;QAC5G,EAAE,IAAI,EAAE,4BAA4B,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,EAAE,gCAAgC,CAAC,EAAE;KAC3G,CAAC;IAEF,0DAA0D;IAC1D,MAAM,cAAc,GAAG;QACnB,EAAE,IAAI,EAAE,kBAAkB,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC,OAAO,EAAE,uBAAuB,CAAC,EAAE;KAC3F,CAAC;IAEF,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;QACzB,IAAI,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,KAAK,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACtD,OAAO,CAAC,IAAI,CAAC,KAAK,KAAK,CAAC,IAAI,SAAS,CAAC,CAAC;QAC3C,CAAC;aAAM,CAAC;YACJ,OAAO,CAAC,IAAI,CAAC,KAAK,KAAK,CAAC,IAAI,cAAc,KAAK,CAAC,IAAI,GAAG,CAAC,CAAC;YACzD,MAAM,EAAE,CAAC;QACb,CAAC;IACL,CAAC;IAED,KAAK,MAAM,KAAK,IAAI,cAAc,EAAE,CAAC;QACjC,IAAI,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,KAAK,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACtD,OAAO,CAAC,IAAI,CAAC,KAAK,KAAK,CAAC,IAAI,SAAS,CAAC,CAAC;QAC3C,CAAC;aAAM,CAAC;YACJ,OAAO,CAAC,IAAI,CAAC,OAAO,KAAK,CAAC,IAAI,eAAe,KAAK,CAAC,IAAI,gCAAgC,CAAC,CAAC;QAC7F,CAAC;IACL,CAAC;IAED,mBAAmB;IACnB,MAAM,cAAc,GAAG,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,4BAA4B,CAAC,CAAC;IAC9E,MAAM,eAAe,GAAG,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,cAAc,CAAC,CAAC;IACjE,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,cAAc,CAAC,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,eAAe,CAAC,EAAE,CAAC;QACpE,OAAO,CAAC,IAAI,CAAC,6CAA6C,CAAC,CAAC;QAC5D,MAAM,EAAE,CAAC;IACb,CAAC;SAAM,CAAC;QACJ,OAAO,CAAC,IAAI,CAAC,uBAAuB,CAAC,CAAC;IAC1C,CAAC;IAED,kBAAkB;IAClB,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,6BAA6B,CAAC,CAAC;IACxE,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,EAAE,CAAC;QAC1B,OAAO,CAAC,IAAI,CAAC,oDAAoD,CAAC,CAAC;QACnE,MAAM,EAAE,CAAC;IACb,CAAC;SAAM,CAAC;QACJ,OAAO,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC;QACnC,OAAO,CAAC,IAAI,CAAC,gCAAgC,CAAC,CAAC;QAC/C,IAAI,CAAC;YACD,QAAQ,CAAC,gBAAgB,OAAO,EAAE,EAAE,EAAE,KAAK,EAAE,MAAM,EAAE,CAAC,CAAC;YACvD,OAAO,CAAC,IAAI,CAAC,4BAA4B,CAAC,CAAC;QAC/C,CAAC;QAAC,MAAM,CAAC;YACL,kEAAkE;YAClE,OAAO,CAAC,IAAI,CAAC,iDAAiD,CAAC,CAAC;QACpE,CAAC;IACL,CAAC;IAED,+CAA+C;IAC/C,qFAAqF;IACrF,8FAA8F;IAC9F,+GAA+G;IAC/G,OAAO,CAAC,IAAI,CAAC,kEAAkE,CAAC,CAAC;IACjF,IAAI,CAAC;QACD,MAAM,aAAa,GAAG,gBAAgB,EAAE,CAAC;QACzC,QAAQ,CAAC,SAAS,aAAa,GAAG,EAAE,EAAE,KAAK,EAAE,MAAM,EAAE,CAAC,CAAC;QACvD,OAAO,CAAC,IAAI,CAAC,0EAA0E,CAAC,CAAC;IAC7F,CAAC;IAAC,MAAM,CAAC;QACL,OAAO,CAAC,IAAI,CAAC,oCAAoC,CAAC,CAAC;QACnD,OAAO,CAAC,IAAI,CAAC,iFAAiF,CAAC,CAAC;QAChG,OAAO,CAAC,IAAI,CAAC,mGAAmG,CAAC,CAAC;QAClH,OAAO,CAAC,IAAI,CAAC,0GAA0G,CAAC,CAAC;QACzH,OAAO,CAAC,IAAI,CAAC,6FAA6F,CAAC,CAAC;QAC5G,MAAM,EAAE,CAAC;IACb,CAAC;IAED,IAAI,MAAM,KAAK,CAAC,EAAE,CAAC;QACf,OAAO,CAAC,IAAI,CAAC,mEAAmE,CAAC,CAAC;IACtF,CAAC;SAAM,CAAC;QACJ,OAAO,CAAC,IAAI,CAAC;YACT,MAAM,2CAA2C,CAAC,CAAC;QACvD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IACpB,CAAC;AACL,CAAC"}

package/dist/src/cli/commands/init.js

@@ -3,14 +3,13 @@ import path from "path";
 import { fileURLToPath } from "url";
 import { execSync } from "child_process";
 import { resolveAdapter, isAdapterShimFile, remapFrameworkContent, runAdapterPostInit, } from "../adapters.js";
-import { mergePackageJson, deepCleanProtocols, sanitizeJson, getPackageVersion, getValidatorPath } from "../utils/pkg.js";
+import { mergePackageJson, deepCleanProtocols, sanitizeJson, getPackageVersion, getValidatorPath, getPackageRoot } from "../utils/pkg.js";
 import { updateGitIgnore, ensureDir, writeJsonFile, copyDir, writeTextFile } from "../utils/fs.js";
 import { initializeMemory } from "../utils/memory.js";
 import { checkCommand } from "./check.js";
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
-const sourceDir = path.join(__dirname, "../../..");
-const targetDir = process.cwd();
+const sourceDir = getPackageRoot();
 const FRAMEWORK_VERSION = getPackageVersion();
 const CORE_FILES = [
     ".enderun",
@@ -117,7 +116,7 @@ const allAgents = [
         instructions: "You are the analyst agent. Independently verify compliance with contracts and specifications between frontend, backend, and the constitution.\n\n🛑 NON-NEGOTIABLE CORE RULES:\n- Independent Stance: Act as an objective verification gate.\n- Contract-First Law: Ensure contract.version.json perfectly matches types.\n- Escalation Priority: Report all contract drift to manager immediately.\n- Surgical Edits: Use replace_text for all document updates."
     }
 ];
-function scaffoldCoreAgents(agentsBaseDir, dryRun) {
+function scaffoldCoreAgents(targetDir, agentsBaseDir, dryRun) {
     ensureDir(agentsBaseDir, dryRun);
     const agentSchemaDir = path.join(agentsBaseDir, "schema");
     ensureDir(agentSchemaDir, dryRun);
@@ -213,8 +212,11 @@ function buildDirsToCreate(adapter) {
     const dirs = [
         adapter.frameworkDir,
         ...FRAMEWORK_SUBDIRS.map((d) => `${adapter.frameworkDir}/${d}`),
-        "apps/web", "apps/backend", "docs", "framework-mcp", "tests",
+        "docs", "framework-mcp",
     ];
+    if (process.env.ENDERUN_SKIP_INSTALL !== "1") {
+        dirs.push("tests");
+    }
     if (adapter.nestedDirs) {
         for (const nested of adapter.nestedDirs)
             dirs.push(`${adapter.frameworkDir}/${nested}`);
@@ -224,6 +226,7 @@ function buildDirsToCreate(adapter) {
     return [...new Set(dirs)];
 }
 export async function initCommand(adapterInput, dryRun = false) {
+    const targetDir = process.cwd();
     const adapter = resolveAdapter(adapterInput);
     const { frameworkDir, shimFile, templateDir } = adapter;
     const targetFrameworkDir = path.join(targetDir, frameworkDir);
@@ -234,11 +237,9 @@ export async function initCommand(adapterInput, dryRun = false) {
     for (const dir of buildDirsToCreate(adapter))
         ensureDir(path.join(targetDir, dir), dryRun);
     const filesToProcess = [...CORE_FILES, shimFile].filter(f => CORE_FILES.includes(f) || f === shimFile || fs.existsSync(path.join(sourceDir, f)));
-    ensureDir(path.join(targetDir, "apps/backend"), dryRun);
-    const initContractPath = path.join(targetDir, "apps/backend/contract.version.json");
-    if (!fs.existsSync(initContractPath)) {
-        writeJsonFile(initContractPath, { contract_hash: "initial_hash_placeholder", last_updated: new Date().toISOString() }, dryRun);
-    }
+    // apps/ directory is intentionally left empty during init.
+    // Users create apps via `agent-enderun create-app` command.
+    // Contract file is created during app scaffolding, not init.
     let targetPkg = {};
     try {
         const targetPkgPath = path.join(targetDir, "package.json");
@@ -314,7 +315,16 @@ export async function initCommand(adapterInput, dryRun = false) {
     if (!dryRun)
         deepCleanProtocols(targetDir, targetScope);
     // Scaffold core agents under the central framework directory
-    scaffoldCoreAgents(path.join(targetFrameworkDir, "agents"), dryRun);
+    let agentFolder = "agents";
+    if (frameworkDir !== ".enderun") {
+        if (adapter.id === "antigravity") {
+            agentFolder = "skills";
+        }
+        else if (adapter.id === "grok") {
+            agentFolder = "plugins";
+        }
+    }
+    scaffoldCoreAgents(targetDir, path.join(targetFrameworkDir, agentFolder), dryRun);
     if (!fs.existsSync(path.join(targetDir, ".git")) && !dryRun) {
         try {
             execSync("git init", { cwd: targetDir, stdio: "ignore" });