refactor(coding-agent): replace AgentSessionRuntimeHost with closure-based AgentSessionRuntime

- Replace AgentSessionRuntimeHost and bootstrap abstractions with AgentSessionRuntime
- Runtime creation is now closure-based via CreateAgentSessionRuntimeFactory
- Factory closes over process-global fixed inputs, recreates cwd-bound services per effective cwd
- Session config (model, thinking, tools, scoped models) re-resolved per target cwd
- CLI resource paths resolved once at startup as absolute paths
- Swap lifecycle: teardown old, create next, apply next (hard fail on creation error)
- Unified diagnostics model (info/warning/error) for args, services, session resolution, resources
- No logging or process exits inside creation/parsing logic
- Removed session_directory support
- Removed session_switch and session_fork extension events (use session_start with reason)
- Moved package/config CLI to package-manager-cli.ts
- Fixed theme init for --resume session picker
- Fixed flaky reftable footer test (content-based polling)
- Fixed silent drop of unknown single-dash CLI flags
- Added error diagnostics for missing explicit CLI resource paths
- Updated SDK docs, examples, plans, exports, tests, changelog

fixes #2753

packages/coding-agent/src/migrations.ts

@@ -6,6 +6,7 @@ import chalk from "chalk";
 import { existsSync, mkdirSync, readdirSync, readFileSync, renameSync, rmSync, writeFileSync } from "fs";
 import { dirname, join } from "path";
 import { CONFIG_DIR_NAME, getAgentDir, getBinDir } from "./config.js";
+import { migrateKeybindingsConfig } from "./core/keybindings.js";
 
 const MIGRATION_GUIDE_URL =
 	"https://github.com/badlogic/pi-mono/blob/main/packages/coding-agent/CHANGELOG.md#extensions-migration";
@@ -152,6 +153,23 @@ function migrateCommandsToPrompts(baseDir: string, label: string): boolean {
 	return false;
 }
 
+function migrateKeybindingsConfigFile(): void {
+	const configPath = join(getAgentDir(), "keybindings.json");
+	if (!existsSync(configPath)) return;
+
+	try {
+		const parsed = JSON.parse(readFileSync(configPath, "utf-8")) as unknown;
+		if (typeof parsed !== "object" || parsed === null || Array.isArray(parsed)) {
+			return;
+		}
+		const { config, migrated } = migrateKeybindingsConfig(parsed as Record<string, unknown>);
+		if (!migrated) return;
+		writeFileSync(configPath, `${JSON.stringify(config, null, 2)}\n`, "utf-8");
+	} catch {
+		// Ignore malformed files during migration
+	}
+}
+
 /**
  * Move fd/rg binaries from tools/ to bin/ if they exist.
  */
@@ -290,6 +308,7 @@ export function runMigrations(cwd: string = process.cwd()): {
 	const migratedAuthProviders = migrateAuthToAuthJson();
 	migrateSessionsFromAgentRoot();
 	migrateToolsToBin();
+	migrateKeybindingsConfigFile();
 	const deprecationWarnings = migrateExtensionSystem(cwd);
 	return { migratedAuthProviders, deprecationWarnings };
 }