Fix --no-skills flag not preventing skills from loading

The --no-skills flag set options.skills = [] in main.ts, but the
interactive mode UI would rediscover skills anyway because it called
loadSkills() directly instead of using the already-loaded skills.

Changes:
- Add AgentSession.skills and AgentSession.skillWarnings properties
- discoverSkills() now returns { skills, warnings } instead of Skill[]
- Interactive mode uses session.skills instead of calling loadSkills()
- Update SDK docs and examples for new return type

Fixes #577

packages/coding-agent/src/core/sdk.ts

@@ -43,7 +43,7 @@ import { ModelRegistry } from "./model-registry.js";
 import { loadPromptTemplates as loadPromptTemplatesInternal, type PromptTemplate } from "./prompt-templates.js";
 import { SessionManager } from "./session-manager.js";
 import { type Settings, SettingsManager, type SkillsSettings } from "./settings-manager.js";
-import { loadSkills as loadSkillsInternal, type Skill } from "./skills.js";
+import { loadSkills as loadSkillsInternal, type Skill, type SkillWarning } from "./skills.js";
 import {
 	buildSystemPrompt as buildSystemPromptInternal,
 	loadProjectContextFiles as loadContextFilesInternal,
@@ -225,13 +225,16 @@ export async function discoverExtensions(
 /**
  * Discover skills from cwd and agentDir.
  */
-export function discoverSkills(cwd?: string, agentDir?: string, settings?: SkillsSettings): Skill[] {
-	const { skills } = loadSkillsInternal({
+export function discoverSkills(
+	cwd?: string,
+	agentDir?: string,
+	settings?: SkillsSettings,
+): { skills: Skill[]; warnings: SkillWarning[] } {
+	return loadSkillsInternal({
 		...settings,
 		cwd: cwd ?? process.cwd(),
 		agentDir: agentDir ?? getDefaultAgentDir(),
 	});
-	return skills;
 }
 
 /**
@@ -419,7 +422,16 @@ export async function createAgentSession(options: CreateAgentSessionOptions = {}
 		thinkingLevel = "off";
 	}
 
-	const skills = options.skills ?? discoverSkills(cwd, agentDir, settingsManager.getSkillsSettings());
+	let skills: Skill[];
+	let skillWarnings: SkillWarning[];
+	if (options.skills !== undefined) {
+		skills = options.skills;
+		skillWarnings = [];
+	} else {
+		const discovered = discoverSkills(cwd, agentDir, settingsManager.getSkillsSettings());
+		skills = discovered.skills;
+		skillWarnings = discovered.warnings;
+	}
 	time("discoverSkills");
 
 	const contextFiles = options.contextFiles ?? discoverContextFiles(cwd, agentDir);
@@ -641,13 +653,6 @@ export async function createAgentSession(options: CreateAgentSessionOptions = {}
 		sessionManager.appendThinkingLevelChange(thinkingLevel);
 	}
 
-	// Determine skillsSettings: if options.skills was explicitly provided (even []),
-	// mark skills as disabled so UI doesn't re-discover them
-	const skillsSettings =
-		options.skills !== undefined
-			? { ...settingsManager.getSkillsSettings(), enabled: false }
-			: settingsManager.getSkillsSettings();
-
 	const session = new AgentSession({
 		agent,
 		sessionManager,
@@ -655,7 +660,9 @@ export async function createAgentSession(options: CreateAgentSessionOptions = {}
 		scopedModels: options.scopedModels,
 		promptTemplates: promptTemplates,
 		extensionRunner,
-		skillsSettings,
+		skills,
+		skillWarnings,
+		skillsSettings: settingsManager.getSkillsSettings(),
 		modelRegistry,
 		toolRegistry: wrappedToolRegistry ?? toolRegistry,
 		rebuildSystemPrompt,