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/resource-loader.ts

@@ -315,6 +315,7 @@ export class DefaultResourceLoader implements ResourceLoader {
 	}
 
 	async reload(): Promise<void> {
+		await this.settingsManager.reload();
 		const resolvedPaths = await this.packageManager.resolve();
 		const cliExtensionPaths = await this.packageManager.resolveExtensionSources(this.additionalExtensionPaths, {
 			temporary: true,
@@ -402,6 +403,11 @@ export class DefaultResourceLoader implements ResourceLoader {
 			extensionsResult.errors.push({ path: conflict.path, error: conflict.message });
 		}
 
+		for (const p of this.additionalExtensionPaths) {
+			if (!existsSync(p)) {
+				extensionsResult.errors.push({ path: p, error: `Extension path does not exist: ${p}` });
+			}
+		}
 		this.extensionsResult = this.extensionsOverride ? this.extensionsOverride(extensionsResult) : extensionsResult;
 		this.applyExtensionSourceInfo(this.extensionsResult.extensions, metadataByPath);
 
@@ -411,6 +417,11 @@ export class DefaultResourceLoader implements ResourceLoader {
 
 		this.lastSkillPaths = skillPaths;
 		this.updateSkillsFromPaths(skillPaths, metadataByPath);
+		for (const p of this.additionalSkillPaths) {
+			if (!existsSync(p) && !this.skillDiagnostics.some((d) => d.path === p)) {
+				this.skillDiagnostics.push({ type: "error", message: "Skill path does not exist", path: p });
+			}
+		}
 
 		const promptPaths = this.noPromptTemplates
 			? this.mergePaths(cliEnabledPrompts, this.additionalPromptTemplatePaths)
@@ -418,6 +429,11 @@ export class DefaultResourceLoader implements ResourceLoader {
 
 		this.lastPromptPaths = promptPaths;
 		this.updatePromptsFromPaths(promptPaths, metadataByPath);
+		for (const p of this.additionalPromptTemplatePaths) {
+			if (!existsSync(p) && !this.promptDiagnostics.some((d) => d.path === p)) {
+				this.promptDiagnostics.push({ type: "error", message: "Prompt template path does not exist", path: p });
+			}
+		}
 
 		const themePaths = this.noThemes
 			? this.mergePaths(cliEnabledThemes, this.additionalThemePaths)
@@ -425,6 +441,11 @@ export class DefaultResourceLoader implements ResourceLoader {
 
 		this.lastThemePaths = themePaths;
 		this.updateThemesFromPaths(themePaths, metadataByPath);
+		for (const p of this.additionalThemePaths) {
+			if (!existsSync(p) && !this.themeDiagnostics.some((d) => d.path === p)) {
+				this.themeDiagnostics.push({ type: "error", message: "Theme path does not exist", path: p });
+			}
+		}
 
 		const agentsFiles = { agentsFiles: loadProjectContextFiles({ cwd: this.cwd, agentDir: this.agentDir }) };
 		const resolvedAgentsFiles = this.agentsFilesOverride ? this.agentsFilesOverride(agentsFiles) : agentsFiles;