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/embedded-commands.ts

@@ -0,0 +1,26 @@
+export interface CommandMatch {
+	fullMatch: string
+	command: string
+	start: number
+	end: number
+}
+
+const COMMAND_PATTERN = /!`([^`]+)`/g
+
+export function findEmbeddedCommands(text: string): CommandMatch[] {
+	const matches: CommandMatch[] = []
+	let match: RegExpExecArray | null
+
+	COMMAND_PATTERN.lastIndex = 0
+
+	while ((match = COMMAND_PATTERN.exec(text)) !== null) {
+		matches.push({
+			fullMatch: match[0],
+			command: match[1],
+			start: match.index,
+			end: match.index + match[0].length,
+		})
+	}
+
+	return matches
+}