refactor: migrate to Turborepo + pnpm + Biome monorepo

Restructure into apps/worker, apps/cli, packages/mcp-server with
Turborepo task orchestration, pnpm workspaces, Biome linting/formatting,
and tsdown CLI bundling.

Key changes:
- src/ -> apps/worker/src/, cli/ -> apps/cli/, mcp-server/ -> packages/mcp-server/
- prompts/ and configs/ moved into apps/worker/
- npm replaced with pnpm, package-lock.json replaced with pnpm-lock.yaml
- Dockerfile updated for pnpm-based builds
- CLI logs command rewritten with chokidar for cross-platform reliability
- Router health checking added for auto-detected router mode
- Centralized path resolution via apps/worker/src/paths.ts

apps/cli/src/commands/uninstall.ts

@@ -0,0 +1,37 @@
+/**
+ * `shn uninstall` command — remove ~/.shannon/ after confirmation (npx only).
+ */
+
+import fs from 'node:fs';
+import os from 'node:os';
+import path from 'node:path';
+import * as p from '@clack/prompts';
+import { stopInfra, stopWorkers } from '../docker.js';
+
+const SHANNON_HOME = path.join(os.homedir(), '.shannon');
+
+export async function uninstall(): Promise<void> {
+  p.intro('Shannon Uninstall');
+
+  if (!fs.existsSync(SHANNON_HOME)) {
+    p.log.info('Nothing to remove. Shannon is not configured on this machine.');
+    p.outro('Done.');
+    return;
+  }
+
+  const confirmed = await p.confirm({
+    message: 'This will permanently remove all past scan data, saved configurations, and API keys. Continue?',
+  });
+  if (p.isCancel(confirmed) || !confirmed) {
+    p.cancel('Aborted.');
+    process.exit(0);
+  }
+
+  // Stop any running containers first
+  stopWorkers();
+  stopInfra(false);
+
+  fs.rmSync(SHANNON_HOME, { recursive: true, force: true });
+  p.log.success('All Shannon data has been removed.');
+  p.outro('Shannon has been uninstalled. Run `npx @keygraph/shannon setup` to start fresh.');
+}