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/resolve-commands-in-text.ts

@@ -0,0 +1,49 @@
+import { executeCommand } from "./execute-command"
+import { findEmbeddedCommands } from "./embedded-commands"
+
+export async function resolveCommandsInText(
+	text: string,
+	depth: number = 0,
+	maxDepth: number = 3,
+): Promise<string> {
+	if (depth >= maxDepth) {
+		return text
+	}
+
+	const matches = findEmbeddedCommands(text)
+	if (matches.length === 0) {
+		return text
+	}
+
+	const tasks = matches.map((m) => executeCommand(m.command))
+	const results = await Promise.allSettled(tasks)
+
+	const replacements = new Map<string, string>()
+
+	matches.forEach((match, idx) => {
+		const result = results[idx]
+		if (result.status === "rejected") {
+			replacements.set(
+				match.fullMatch,
+				`[error: ${
+					result.reason instanceof Error
+						? result.reason.message
+						: String(result.reason)
+				}]`,
+			)
+		} else {
+			replacements.set(match.fullMatch, result.value)
+		}
+	})
+
+	let resolved = text
+	for (const [pattern, replacement] of replacements.entries()) {
+		resolved = resolved.split(pattern).join(replacement)
+	}
+
+	if (findEmbeddedCommands(resolved).length > 0) {
+		return resolveCommandsInText(resolved, depth + 1, maxDepth)
+	}
+
+	return resolved
+}