refactor(mcp): remove scaffolding tools (createApp, createDatabase, setupAppSchema)

Scaffolding now happens outside Claude Code via `crayon init` / `crayon local run`,
so these MCP tools are no longer needed.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: cevian

CLAUDE.md

@@ -35,9 +35,8 @@ claude --plugin-dir /path/to/crayon
 
 ### MCP Tools
 
-12 tools exposed via `scripts/run-mcp.cjs` (prefixed `mcp__plugin_crayon_crayon-local-tools__`):
+9 tools exposed via MCP (crayon-sandbox):
 
-- `createApp` / `createDatabase` / `setupAppSchema` - Project scaffolding
 - `listIntegrations` / `getConnectionInfo` - OAuth connection management
 - `listWorkflows` / `runWorkflow` / `runNode` - Workflow execution
 - `listRuns` / `getRun` / `getTrace` - Run history and tracing
@@ -59,7 +58,7 @@ claude --plugin-dir /path/to/crayon
 | User node | `src/crayon/nodes/` in app | Custom logic functions |
 | Agent | `src/crayon/agents/` in app (.ts + colocated .md spec) | AI reasoning via Vercel AI SDK |
 
-### App Template Structure (scaffolded by `createApp`)
+### App Template Structure (scaffolded by `crayon init`)
 
 ```
 my-app/

packages/core/src/cli/mcp/tools/createApp.ts

@@ -1,6 +1,3 @@
-import { createAppFactory } from "./createApp.js";
-import { createDatabaseFactory } from "./createDatabase.js";
-import { setupAppSchemaFactory } from "./setupAppSchema.js";
 import { listIntegrationsFactory } from "./listIntegrations.js";
 import { getConnectionInfoFactory } from "./getConnectionInfo.js";
 
@@ -14,9 +11,6 @@ import { getSkillGuideFactory } from "./getSkillGuide.js";
 
 export async function getApiFactories() {
   return [
-    createAppFactory,
-    createDatabaseFactory,
-    setupAppSchemaFactory,
     listIntegrationsFactory,
     getConnectionInfoFactory,