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/tmux/tmux-utils/pane-close.ts

@@ -0,0 +1,48 @@
+import { spawn } from "bun"
+import { getTmuxPath } from "../../../tools/interactive-bash/tmux-path-resolver"
+import { isInsideTmux } from "./environment"
+
+function delay(milliseconds: number): Promise<void> {
+	return new Promise((resolve) => setTimeout(resolve, milliseconds))
+}
+
+export async function closeTmuxPane(paneId: string): Promise<boolean> {
+	const { log } = await import("../../logger")
+
+	if (!isInsideTmux()) {
+		log("[closeTmuxPane] SKIP: not inside tmux")
+		return false
+	}
+
+	const tmux = await getTmuxPath()
+	if (!tmux) {
+		log("[closeTmuxPane] SKIP: tmux not found")
+		return false
+	}
+
+	log("[closeTmuxPane] sending Ctrl+C for graceful shutdown", { paneId })
+	const ctrlCProc = spawn([tmux, "send-keys", "-t", paneId, "C-c"], {
+		stdout: "pipe",
+		stderr: "pipe",
+	})
+	await ctrlCProc.exited
+
+	await delay(250)
+
+	log("[closeTmuxPane] killing pane", { paneId })
+
+	const proc = spawn([tmux, "kill-pane", "-t", paneId], {
+		stdout: "pipe",
+		stderr: "pipe",
+	})
+	const exitCode = await proc.exited
+	const stderr = await new Response(proc.stderr).text()
+
+	if (exitCode !== 0) {
+		log("[closeTmuxPane] FAILED", { paneId, exitCode, stderr: stderr.trim() })
+	} else {
+		log("[closeTmuxPane] SUCCESS", { paneId })
+	}
+
+	return exitCode === 0
+}