refactor: Restructure monorepo to apps/server/ and apps/web/ layout

Move src/ → apps/server/ and packages/web/ → apps/web/ to adopt
standard monorepo conventions (apps/ for runnable apps, packages/
for reusable libraries). Update all config files, shared package
imports, test fixtures, and documentation to reflect new paths.

Key fixes:
- Update workspace config to ["apps/*", "packages/*"]
- Update tsconfig.json rootDir/include for apps/server/
- Add apps/web/** to vitest exclude list
- Update drizzle.config.ts schema path
- Fix ensure-schema.ts migration path detection (3 levels up in dev,
  2 levels up in dist)
- Fix tests/integration/cli-server.test.ts import paths
- Update packages/shared imports to apps/server/ paths
- Update all docs/ files with new paths

apps/server/git/project-clones.ts

@@ -0,0 +1,48 @@
+/**
+ * Project Clone Management
+ *
+ * Ensures project repositories are cloned into the repos/ directory.
+ * These base clones are used as the source for git worktrees.
+ */
+
+import { join } from 'node:path';
+import { access } from 'node:fs/promises';
+import { cloneProject } from './clone.js';
+import { createModuleLogger } from '../logger/index.js';
+
+const log = createModuleLogger('git');
+
+/**
+ * Derive the canonical clone directory for a project (relative to workspace root).
+ * Convention: repos/<sanitizedName>-<id>/
+ */
+export function getProjectCloneDir(projectName: string, projectId: string): string {
+  const sanitized = projectName.toLowerCase().replace(/[^a-z0-9]+/g, '-').replace(/^-|-$/g, '');
+  return join('repos', `${sanitized}-${projectId}`);
+}
+
+/**
+ * Ensure a project's git repository is cloned to the workspace.
+ * Uses the canonical path: <workspaceRoot>/repos/<sanitizedName>-<id>/
+ *
+ * @param project - Project with id, name, and url
+ * @param workspaceRoot - Absolute path to the workspace root
+ * @returns Absolute path to the clone directory
+ */
+export async function ensureProjectClone(
+  project: { id: string; name: string; url: string },
+  workspaceRoot: string,
+): Promise<string> {
+  const relPath = getProjectCloneDir(project.name, project.id);
+  const clonePath = join(workspaceRoot, relPath);
+
+  try {
+    await access(clonePath);
+    log.debug({ project: project.name, clonePath }, 'project clone already exists');
+    return clonePath;
+  } catch {
+    log.info({ project: project.name, url: project.url, clonePath }, 'cloning project for first time');
+    await cloneProject(project.url, clonePath);
+    return clonePath;
+  }
+}