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/core/package-manager.ts

@@ -57,11 +57,21 @@ export interface PackageUpdate {
 	scope: Exclude<SourceScope, "temporary">;
 }
 
+export interface ConfiguredPackage {
+	source: string;
+	scope: "user" | "project";
+	filtered: boolean;
+	installedPath?: string;
+}
+
 export interface PackageManager {
 	resolve(onMissing?: (source: string) => Promise<MissingSourceAction>): Promise<ResolvedPaths>;
 	install(source: string, options?: { local?: boolean }): Promise<void>;
+	installAndPersist(source: string, options?: { local?: boolean }): Promise<void>;
 	remove(source: string, options?: { local?: boolean }): Promise<void>;
+	removeAndPersist(source: string, options?: { local?: boolean }): Promise<boolean>;
 	update(source?: string): Promise<void>;
+	listConfiguredPackages(): ConfiguredPackage[];
 	resolveExtensionSources(
 		sources: string[],
 		options?: { local?: boolean; temporary?: boolean },
@@ -837,6 +847,34 @@ export class DefaultPackageManager implements PackageManager {
 		return this.toResolvedPaths(accumulator);
 	}
 
+	listConfiguredPackages(): ConfiguredPackage[] {
+		const globalSettings = this.settingsManager.getGlobalSettings();
+		const projectSettings = this.settingsManager.getProjectSettings();
+		const configuredPackages: ConfiguredPackage[] = [];
+
+		for (const pkg of globalSettings.packages ?? []) {
+			const source = typeof pkg === "string" ? pkg : pkg.source;
+			configuredPackages.push({
+				source,
+				scope: "user",
+				filtered: typeof pkg === "object",
+				installedPath: this.getInstalledPath(source, "user"),
+			});
+		}
+
+		for (const pkg of projectSettings.packages ?? []) {
+			const source = typeof pkg === "string" ? pkg : pkg.source;
+			configuredPackages.push({
+				source,
+				scope: "project",
+				filtered: typeof pkg === "object",
+				installedPath: this.getInstalledPath(source, "project"),
+			});
+		}
+
+		return configuredPackages;
+	}
+
 	async install(source: string, options?: { local?: boolean }): Promise<void> {
 		const parsed = this.parseSource(source);
 		const scope: SourceScope = options?.local ? "project" : "user";
@@ -860,6 +898,11 @@ export class DefaultPackageManager implements PackageManager {
 		});
 	}
 
+	async installAndPersist(source: string, options?: { local?: boolean }): Promise<void> {
+		await this.install(source, options);
+		this.addSourceToSettings(source, options);
+	}
+
 	async remove(source: string, options?: { local?: boolean }): Promise<void> {
 		const parsed = this.parseSource(source);
 		const scope: SourceScope = options?.local ? "project" : "user";
@@ -879,6 +922,11 @@ export class DefaultPackageManager implements PackageManager {
 		});
 	}
 
+	async removeAndPersist(source: string, options?: { local?: boolean }): Promise<boolean> {
+		await this.remove(source, options);
+		return this.removeSourceFromSettings(source, options);
+	}
+
 	async update(source?: string): Promise<void> {
 		const globalSettings = this.settingsManager.getGlobalSettings();
 		const projectSettings = this.settingsManager.getProjectSettings();