refactor: wave 2 - split atlas, auto-update-checker, session-recovery, todo-enforcer, background-task hooks

- Extract atlas/ into 15 focused modules (hook, event handler, tool policies, types, etc.)
- Split auto-update-checker into checker/ and hook/ subdirectories with single-purpose files
- Decompose session-recovery into separate recovery strategy files per error type
- Extract todo-continuation-enforcer from monolith to directory with dedicated modules
- Split background-task/tools.ts into individual tool creator files
- Extract command-executor, tmux-utils into focused sub-modules
- Split config/schema.ts into domain-specific schema files
- Decompose cli/config-manager.ts into focused modules
- Rollback skill-mcp-manager, model-availability, index.ts splits that broke tests
- Fix all import path depths for moved files (../../ -> ../../../)
- Add explicit type annotations to resolve TS7006 implicit any errors

Typecheck: 0 errors
Tests: 2359 pass, 5 fail (all pre-existing)

src/shared/command-executor/execute-command.ts

@@ -0,0 +1,28 @@
+import { exec } from "node:child_process"
+import { promisify } from "node:util"
+
+const execAsync = promisify(exec)
+
+type ExecError = { stdout?: Buffer; stderr?: Buffer; message?: string }
+
+export async function executeCommand(command: string): Promise<string> {
+	try {
+		const { stdout, stderr } = await execAsync(command)
+
+		const out = stdout?.toString().trim() ?? ""
+		const err = stderr?.toString().trim() ?? ""
+
+		if (err) {
+			return out ? `${out}\n[stderr: ${err}]` : `[stderr: ${err}]`
+		}
+
+		return out
+	} catch (error: unknown) {
+		const e = error as ExecError
+		const stdout = e?.stdout?.toString().trim() ?? ""
+		const stderr = e?.stderr?.toString().trim() ?? ""
+		const errorMessage = stderr || e?.message || String(error)
+
+		return stdout ? `${stdout}\n[stderr: ${errorMessage}]` : `[stderr: ${errorMessage}]`
+	}
+}