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-hook-command.ts

@@ -0,0 +1,78 @@
+import { spawn } from "node:child_process"
+import { getHomeDirectory } from "./home-directory"
+import { findBashPath, findZshPath } from "./shell-path"
+
+export interface CommandResult {
+	exitCode: number
+	stdout?: string
+	stderr?: string
+}
+
+export interface ExecuteHookOptions {
+	forceZsh?: boolean
+	zshPath?: string
+}
+
+export async function executeHookCommand(
+	command: string,
+	stdin: string,
+	cwd: string,
+	options?: ExecuteHookOptions,
+): Promise<CommandResult> {
+	const home = getHomeDirectory()
+
+	const expandedCommand = command
+		.replace(/^~(?=\/|$)/g, home)
+		.replace(/\s~(?=\/)/g, ` ${home}`)
+		.replace(/\$CLAUDE_PROJECT_DIR/g, cwd)
+		.replace(/\$\{CLAUDE_PROJECT_DIR\}/g, cwd)
+
+	let finalCommand = expandedCommand
+
+	if (options?.forceZsh) {
+		const zshPath = findZshPath(options.zshPath)
+		const escapedCommand = expandedCommand.replace(/'/g, "'\\''")
+		if (zshPath) {
+			finalCommand = `${zshPath} -lc '${escapedCommand}'`
+		} else {
+			const bashPath = findBashPath()
+			if (bashPath) {
+				finalCommand = `${bashPath} -lc '${escapedCommand}'`
+			}
+		}
+	}
+
+	return new Promise((resolve) => {
+		const proc = spawn(finalCommand, {
+			cwd,
+			shell: true,
+			env: { ...process.env, HOME: home, CLAUDE_PROJECT_DIR: cwd },
+		})
+
+		let stdout = ""
+		let stderr = ""
+
+		proc.stdout?.on("data", (data) => {
+			stdout += data.toString()
+		})
+
+		proc.stderr?.on("data", (data) => {
+			stderr += data.toString()
+		})
+
+		proc.stdin?.write(stdin)
+		proc.stdin?.end()
+
+		proc.on("close", (code) => {
+			resolve({
+				exitCode: code ?? 0,
+				stdout: stdout.trim(),
+				stderr: stderr.trim(),
+			})
+		})
+
+		proc.on("error", (err) => {
+			resolve({ exitCode: 1, stderr: err.message })
+		})
+	})
+}