pi-oxidized 0.1.1

package/.references/pi/packages/coding-agent/src/core/resource-loader.ts

@@ -0,0 +1,1039 @@
+import { existsSync, readdirSync, readFileSync, statSync } from "node:fs";
+import { dirname, join, resolve, sep } from "node:path";
+import chalk from "chalk";
+import { CONFIG_DIR_NAME } from "../config.ts";
+import { loadThemeFromPath, type Theme } from "../modes/interactive/theme/theme.ts";
+import type { ResourceDiagnostic } from "./diagnostics.ts";
+
+export type { ResourceCollision, ResourceDiagnostic } from "./diagnostics.ts";
+
+import { canonicalizePath, isLocalPath, resolvePath } from "../utils/paths.ts";
+import { createEventBus, type EventBus } from "./event-bus.ts";
+import {
+	clearExtensionCache,
+	createExtensionRuntime,
+	loadExtensionFromFactory,
+	loadExtensionsCached,
+} from "./extensions/loader.ts";
+import type { Extension, ExtensionRuntime, InlineExtension, LoadExtensionsResult } from "./extensions/types.ts";
+import { DefaultPackageManager, type PathMetadata, type ResolvedResource } from "./package-manager.ts";
+import type { PromptTemplate } from "./prompt-templates.ts";
+import { loadPromptTemplates } from "./prompt-templates.ts";
+import { SettingsManager } from "./settings-manager.ts";
+import type { Skill } from "./skills.ts";
+import { loadSkills } from "./skills.ts";
+import { createSourceInfo, type SourceInfo } from "./source-info.ts";
+import { resetTimings } from "./timings.ts";
+
+export interface ResourceExtensionPaths {
+	skillPaths?: Array<{ path: string; metadata: PathMetadata }>;
+	promptPaths?: Array<{ path: string; metadata: PathMetadata }>;
+	themePaths?: Array<{ path: string; metadata: PathMetadata }>;
+}
+
+export interface ResourceLoaderReloadOptions {
+	resolveProjectTrust?: (input: { extensionsResult: LoadExtensionsResult }) => Promise<boolean>;
+}
+
+export interface ResourceLoader {
+	getExtensions(): LoadExtensionsResult;
+	getSkills(): { skills: Skill[]; diagnostics: ResourceDiagnostic[] };
+	getPrompts(): { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] };
+	getThemes(): { themes: Theme[]; diagnostics: ResourceDiagnostic[] };
+	getAgentsFiles(): { agentsFiles: Array<{ path: string; content: string }> };
+	getSystemPrompt(): string | undefined;
+	getAppendSystemPrompt(): string[];
+	extendResources(paths: ResourceExtensionPaths): void;
+	reload(options?: ResourceLoaderReloadOptions): Promise<void>;
+}
+
+function resolvePromptInput(input: string | undefined, description: string): string | undefined {
+	if (!input) {
+		return undefined;
+	}
+
+	if (existsSync(input)) {
+		try {
+			return readFileSync(input, "utf-8");
+		} catch (error) {
+			console.error(chalk.yellow(`Warning: Could not read ${description} file ${input}: ${error}`));
+			return input;
+		}
+	}
+
+	return input;
+}
+
+function loadContextFileFromDir(dir: string): { path: string; content: string } | null {
+	const candidates = ["AGENTS.md", "AGENTS.MD", "CLAUDE.md", "CLAUDE.MD"];
+	for (const filename of candidates) {
+		const filePath = join(dir, filename);
+		if (existsSync(filePath)) {
+			try {
+				return {
+					path: filePath,
+					content: readFileSync(filePath, "utf-8"),
+				};
+			} catch (error) {
+				console.error(chalk.yellow(`Warning: Could not read ${filePath}: ${error}`));
+			}
+		}
+	}
+	return null;
+}
+
+export function loadProjectContextFiles(options: {
+	cwd: string;
+	agentDir: string;
+}): Array<{ path: string; content: string }> {
+	const resolvedCwd = resolvePath(options.cwd);
+	const resolvedAgentDir = resolvePath(options.agentDir);
+
+	const contextFiles: Array<{ path: string; content: string }> = [];
+	const seenPaths = new Set<string>();
+
+	const globalContext = loadContextFileFromDir(resolvedAgentDir);
+	if (globalContext) {
+		contextFiles.push(globalContext);
+		seenPaths.add(globalContext.path);
+	}
+
+	const ancestorContextFiles: Array<{ path: string; content: string }> = [];
+
+	let currentDir = resolvedCwd;
+
+	while (true) {
+		const contextFile = loadContextFileFromDir(currentDir);
+		if (contextFile && !seenPaths.has(contextFile.path)) {
+			ancestorContextFiles.unshift(contextFile);
+			seenPaths.add(contextFile.path);
+		}
+
+		const parentDir = dirname(currentDir);
+		if (parentDir === currentDir) break;
+		currentDir = parentDir;
+	}
+
+	contextFiles.push(...ancestorContextFiles);
+
+	return contextFiles;
+}
+
+export interface DefaultResourceLoaderOptions {
+	cwd: string;
+	agentDir: string;
+	settingsManager?: SettingsManager;
+	eventBus?: EventBus;
+	additionalExtensionPaths?: string[];
+	additionalSkillPaths?: string[];
+	additionalPromptTemplatePaths?: string[];
+	additionalThemePaths?: string[];
+	extensionFactories?: InlineExtension[];
+	noExtensions?: boolean;
+	noSkills?: boolean;
+	noPromptTemplates?: boolean;
+	noThemes?: boolean;
+	noContextFiles?: boolean;
+	systemPrompt?: string;
+	appendSystemPrompt?: string[];
+	extensionsOverride?: (base: LoadExtensionsResult) => LoadExtensionsResult;
+	skillsOverride?: (base: { skills: Skill[]; diagnostics: ResourceDiagnostic[] }) => {
+		skills: Skill[];
+		diagnostics: ResourceDiagnostic[];
+	};
+	promptsOverride?: (base: { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] }) => {
+		prompts: PromptTemplate[];
+		diagnostics: ResourceDiagnostic[];
+	};
+	themesOverride?: (base: { themes: Theme[]; diagnostics: ResourceDiagnostic[] }) => {
+		themes: Theme[];
+		diagnostics: ResourceDiagnostic[];
+	};
+	agentsFilesOverride?: (base: { agentsFiles: Array<{ path: string; content: string }> }) => {
+		agentsFiles: Array<{ path: string; content: string }>;
+	};
+	systemPromptOverride?: (base: string | undefined) => string | undefined;
+	appendSystemPromptOverride?: (base: string[]) => string[];
+}
+
+export class DefaultResourceLoader implements ResourceLoader {
+	private cwd: string;
+	private agentDir: string;
+	private settingsManager: SettingsManager;
+	private eventBus: EventBus;
+	private packageManager: DefaultPackageManager;
+	private additionalExtensionPaths: string[];
+	private additionalSkillPaths: string[];
+	private additionalPromptTemplatePaths: string[];
+	private additionalThemePaths: string[];
+	private extensionFactories: InlineExtension[];
+	private noExtensions: boolean;
+	private noSkills: boolean;
+	private noPromptTemplates: boolean;
+	private noThemes: boolean;
+	private noContextFiles: boolean;
+	private systemPromptSource?: string;
+	private appendSystemPromptSource?: string[];
+	private extensionsOverride?: (base: LoadExtensionsResult) => LoadExtensionsResult;
+	private skillsOverride?: (base: { skills: Skill[]; diagnostics: ResourceDiagnostic[] }) => {
+		skills: Skill[];
+		diagnostics: ResourceDiagnostic[];
+	};
+	private promptsOverride?: (base: { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] }) => {
+		prompts: PromptTemplate[];
+		diagnostics: ResourceDiagnostic[];
+	};
+	private themesOverride?: (base: { themes: Theme[]; diagnostics: ResourceDiagnostic[] }) => {
+		themes: Theme[];
+		diagnostics: ResourceDiagnostic[];
+	};
+	private agentsFilesOverride?: (base: { agentsFiles: Array<{ path: string; content: string }> }) => {
+		agentsFiles: Array<{ path: string; content: string }>;
+	};
+	private systemPromptOverride?: (base: string | undefined) => string | undefined;
+	private appendSystemPromptOverride?: (base: string[]) => string[];
+
+	private extensionsResult: LoadExtensionsResult;
+	private skills: Skill[];
+	private skillDiagnostics: ResourceDiagnostic[];
+	private prompts: PromptTemplate[];
+	private promptDiagnostics: ResourceDiagnostic[];
+	private themes: Theme[];
+	private themeDiagnostics: ResourceDiagnostic[];
+	private agentsFiles: Array<{ path: string; content: string }>;
+	private systemPrompt?: string;
+	private appendSystemPrompt: string[];
+	private lastSkillPaths: string[];
+	private extensionSkillSourceInfos: Map<string, SourceInfo>;
+	private extensionPromptSourceInfos: Map<string, SourceInfo>;
+	private extensionThemeSourceInfos: Map<string, SourceInfo>;
+	private lastPromptPaths: string[];
+	private lastThemePaths: string[];
+	private loaded: boolean;
+
+	constructor(options: DefaultResourceLoaderOptions) {
+		this.cwd = resolvePath(options.cwd);
+		this.agentDir = resolvePath(options.agentDir);
+		this.settingsManager = options.settingsManager ?? SettingsManager.create(this.cwd, this.agentDir);
+		this.eventBus = options.eventBus ?? createEventBus();
+		this.packageManager = new DefaultPackageManager({
+			cwd: this.cwd,
+			agentDir: this.agentDir,
+			settingsManager: this.settingsManager,
+		});
+		this.additionalExtensionPaths = options.additionalExtensionPaths ?? [];
+		this.additionalSkillPaths = options.additionalSkillPaths ?? [];
+		this.additionalPromptTemplatePaths = options.additionalPromptTemplatePaths ?? [];
+		this.additionalThemePaths = options.additionalThemePaths ?? [];
+		this.extensionFactories = options.extensionFactories ?? [];
+		this.noExtensions = options.noExtensions ?? false;
+		this.noSkills = options.noSkills ?? false;
+		this.noPromptTemplates = options.noPromptTemplates ?? false;
+		this.noThemes = options.noThemes ?? false;
+		this.noContextFiles = options.noContextFiles ?? false;
+		this.systemPromptSource = options.systemPrompt;
+		this.appendSystemPromptSource = options.appendSystemPrompt;
+		this.extensionsOverride = options.extensionsOverride;
+		this.skillsOverride = options.skillsOverride;
+		this.promptsOverride = options.promptsOverride;
+		this.themesOverride = options.themesOverride;
+		this.agentsFilesOverride = options.agentsFilesOverride;
+		this.systemPromptOverride = options.systemPromptOverride;
+		this.appendSystemPromptOverride = options.appendSystemPromptOverride;
+
+		this.extensionsResult = { extensions: [], errors: [], runtime: createExtensionRuntime() };
+		this.skills = [];
+		this.skillDiagnostics = [];
+		this.prompts = [];
+		this.promptDiagnostics = [];
+		this.themes = [];
+		this.themeDiagnostics = [];
+		this.agentsFiles = [];
+		this.appendSystemPrompt = [];
+		this.lastSkillPaths = [];
+		this.extensionSkillSourceInfos = new Map();
+		this.extensionPromptSourceInfos = new Map();
+		this.extensionThemeSourceInfos = new Map();
+		this.lastPromptPaths = [];
+		this.lastThemePaths = [];
+		this.loaded = false;
+	}
+
+	getExtensions(): LoadExtensionsResult {
+		return this.extensionsResult;
+	}
+
+	getSkills(): { skills: Skill[]; diagnostics: ResourceDiagnostic[] } {
+		return { skills: this.skills, diagnostics: this.skillDiagnostics };
+	}
+
+	getPrompts(): { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] } {
+		return { prompts: this.prompts, diagnostics: this.promptDiagnostics };
+	}
+
+	getThemes(): { themes: Theme[]; diagnostics: ResourceDiagnostic[] } {
+		return { themes: this.themes, diagnostics: this.themeDiagnostics };
+	}
+
+	getAgentsFiles(): { agentsFiles: Array<{ path: string; content: string }> } {
+		return { agentsFiles: this.agentsFiles };
+	}
+
+	getSystemPrompt(): string | undefined {
+		return this.systemPrompt;
+	}
+
+	getAppendSystemPrompt(): string[] {
+		return this.appendSystemPrompt;
+	}
+
+	extendResources(paths: ResourceExtensionPaths): void {
+		const skillPaths = this.normalizeExtensionPaths(paths.skillPaths ?? []);
+		const promptPaths = this.normalizeExtensionPaths(paths.promptPaths ?? []);
+		const themePaths = this.normalizeExtensionPaths(paths.themePaths ?? []);
+
+		for (const entry of skillPaths) {
+			this.extensionSkillSourceInfos.set(entry.path, createSourceInfo(entry.path, entry.metadata));
+		}
+		for (const entry of promptPaths) {
+			this.extensionPromptSourceInfos.set(entry.path, createSourceInfo(entry.path, entry.metadata));
+		}
+		for (const entry of themePaths) {
+			this.extensionThemeSourceInfos.set(entry.path, createSourceInfo(entry.path, entry.metadata));
+		}
+
+		if (skillPaths.length > 0) {
+			this.lastSkillPaths = this.mergePaths(
+				this.lastSkillPaths,
+				skillPaths.map((entry) => entry.path),
+			);
+			this.updateSkillsFromPaths(this.lastSkillPaths);
+		}
+
+		if (promptPaths.length > 0) {
+			this.lastPromptPaths = this.mergePaths(
+				this.lastPromptPaths,
+				promptPaths.map((entry) => entry.path),
+			);
+			this.updatePromptsFromPaths(this.lastPromptPaths);
+		}
+
+		if (themePaths.length > 0) {
+			this.lastThemePaths = this.mergePaths(
+				this.lastThemePaths,
+				themePaths.map((entry) => entry.path),
+			);
+			this.updateThemesFromPaths(this.lastThemePaths);
+		}
+	}
+
+	async loadProjectTrustExtensions(): Promise<LoadExtensionsResult> {
+		// Force untrusted project settings for the bootstrap pass. This keeps project-local
+		// extensions/packages out while still loading user/global and temporary CLI extensions.
+		this.settingsManager.setProjectTrusted(false);
+		await this.settingsManager.reload();
+		return this.loadCurrentExtensionSet({ includeInlineFactories: true });
+	}
+
+	async reload(options?: ResourceLoaderReloadOptions): Promise<void> {
+		resetTimings("extensions");
+
+		if (this.loaded) {
+			clearExtensionCache();
+		}
+
+		let preTrustExtensions: LoadExtensionsResult | undefined;
+		if (options?.resolveProjectTrust) {
+			preTrustExtensions = await this.loadProjectTrustExtensions();
+			const projectTrusted = await options.resolveProjectTrust({ extensionsResult: preTrustExtensions });
+			this.settingsManager.setProjectTrusted(projectTrusted);
+		}
+
+		// reload() preserves SettingsManager.projectTrusted and reloads settings for that trust state.
+		await this.settingsManager.reload();
+		const resolvedPaths = await this.packageManager.resolve();
+		const cliExtensionPaths = await this.packageManager.resolveExtensionSources(this.additionalExtensionPaths, {
+			temporary: true,
+		});
+		const metadataByPath = new Map<string, PathMetadata>();
+
+		this.extensionSkillSourceInfos = new Map();
+		this.extensionPromptSourceInfos = new Map();
+		this.extensionThemeSourceInfos = new Map();
+
+		// Helper to extract enabled paths and store metadata
+		const getEnabledResources = (resources: ResolvedResource[]): ResolvedResource[] => {
+			for (const r of resources) {
+				if (!metadataByPath.has(r.path)) {
+					metadataByPath.set(r.path, r.metadata);
+				}
+			}
+			return resources.filter((r) => r.enabled);
+		};
+
+		const getEnabledPaths = (resources: ResolvedResource[]): string[] =>
+			getEnabledResources(resources).map((r) => r.path);
+		const enabledExtensions = getEnabledPaths(resolvedPaths.extensions);
+		const enabledSkillResources = getEnabledResources(resolvedPaths.skills);
+		const enabledPrompts = getEnabledPaths(resolvedPaths.prompts);
+		const enabledThemes = getEnabledPaths(resolvedPaths.themes);
+
+		const enabledSkills = enabledSkillResources.map((resource) => this.mapSkillPath(resource, metadataByPath));
+
+		// Add CLI paths metadata
+		for (const r of cliExtensionPaths.extensions) {
+			if (!metadataByPath.has(r.path)) {
+				metadataByPath.set(r.path, { source: "cli", scope: "temporary", origin: "top-level" });
+			}
+		}
+		for (const r of cliExtensionPaths.skills) {
+			if (!metadataByPath.has(r.path)) {
+				metadataByPath.set(r.path, { source: "cli", scope: "temporary", origin: "top-level" });
+			}
+		}
+
+		const cliEnabledExtensions = getEnabledPaths(cliExtensionPaths.extensions);
+		const cliEnabledSkills = getEnabledPaths(cliExtensionPaths.skills);
+		const cliEnabledPrompts = getEnabledPaths(cliExtensionPaths.prompts);
+		const cliEnabledThemes = getEnabledPaths(cliExtensionPaths.themes);
+
+		const extensionPaths = this.noExtensions
+			? cliEnabledExtensions
+			: this.mergePaths(cliEnabledExtensions, enabledExtensions);
+
+		const extensionsResult = await this.loadFinalExtensionSet(extensionPaths, preTrustExtensions);
+		for (const p of this.additionalExtensionPaths) {
+			if (isLocalPath(p)) {
+				const resolved = this.resolveResourcePath(p);
+				if (!existsSync(resolved)) {
+					extensionsResult.errors.push({ path: resolved, error: `Extension path does not exist: ${resolved}` });
+				}
+			}
+		}
+		this.extensionsResult = this.extensionsOverride ? this.extensionsOverride(extensionsResult) : extensionsResult;
+		this.applyExtensionSourceInfo(this.extensionsResult.extensions, metadataByPath);
+
+		const skillPaths = this.noSkills
+			? this.mergePaths(cliEnabledSkills, this.additionalSkillPaths)
+			: this.mergePaths([...cliEnabledSkills, ...enabledSkills], this.additionalSkillPaths);
+
+		this.lastSkillPaths = skillPaths;
+		this.updateSkillsFromPaths(skillPaths, metadataByPath);
+		for (const p of this.additionalSkillPaths) {
+			if (isLocalPath(p)) {
+				const resolved = this.resolveResourcePath(p);
+				if (!existsSync(resolved) && !this.skillDiagnostics.some((d) => d.path === resolved)) {
+					this.skillDiagnostics.push({ type: "error", message: "Skill path does not exist", path: resolved });
+				}
+			}
+		}
+
+		const promptPaths = this.noPromptTemplates
+			? this.mergePaths(cliEnabledPrompts, this.additionalPromptTemplatePaths)
+			: this.mergePaths([...cliEnabledPrompts, ...enabledPrompts], this.additionalPromptTemplatePaths);
+
+		this.lastPromptPaths = promptPaths;
+		this.updatePromptsFromPaths(promptPaths, metadataByPath);
+		for (const p of this.additionalPromptTemplatePaths) {
+			if (isLocalPath(p)) {
+				const resolved = this.resolveResourcePath(p);
+				if (!existsSync(resolved) && !this.promptDiagnostics.some((d) => d.path === resolved)) {
+					this.promptDiagnostics.push({
+						type: "error",
+						message: "Prompt template path does not exist",
+						path: resolved,
+					});
+				}
+			}
+		}
+
+		const themePaths = this.noThemes
+			? this.mergePaths(cliEnabledThemes, this.additionalThemePaths)
+			: this.mergePaths([...cliEnabledThemes, ...enabledThemes], this.additionalThemePaths);
+
+		this.lastThemePaths = themePaths;
+		this.updateThemesFromPaths(themePaths, metadataByPath);
+		for (const p of this.additionalThemePaths) {
+			const resolved = this.resolveResourcePath(p);
+			if (!existsSync(resolved) && !this.themeDiagnostics.some((d) => d.path === resolved)) {
+				this.themeDiagnostics.push({ type: "error", message: "Theme path does not exist", path: resolved });
+			}
+		}
+
+		const agentsFiles = {
+			agentsFiles: this.noContextFiles
+				? []
+				: loadProjectContextFiles({
+						cwd: this.cwd,
+						agentDir: this.agentDir,
+					}),
+		};
+		const resolvedAgentsFiles = this.agentsFilesOverride ? this.agentsFilesOverride(agentsFiles) : agentsFiles;
+		this.agentsFiles = resolvedAgentsFiles.agentsFiles;
+
+		const baseSystemPrompt = resolvePromptInput(
+			this.systemPromptSource ?? this.discoverSystemPromptFile(),
+			"system prompt",
+		);
+		this.systemPrompt = this.systemPromptOverride ? this.systemPromptOverride(baseSystemPrompt) : baseSystemPrompt;
+
+		const appendSources =
+			this.appendSystemPromptSource ??
+			(this.discoverAppendSystemPromptFile() ? [this.discoverAppendSystemPromptFile()!] : []);
+		const baseAppend = appendSources
+			.map((s) => resolvePromptInput(s, "append system prompt"))
+			.filter((s): s is string => s !== undefined);
+		this.appendSystemPrompt = this.appendSystemPromptOverride
+			? this.appendSystemPromptOverride(baseAppend)
+			: baseAppend;
+		this.loaded = true;
+	}
+
+	private async loadCurrentExtensionSet(options: { includeInlineFactories: boolean }): Promise<LoadExtensionsResult> {
+		const resolvedPaths = await this.packageManager.resolve();
+		const cliExtensionPaths = await this.packageManager.resolveExtensionSources(this.additionalExtensionPaths, {
+			temporary: true,
+		});
+		const enabledExtensions = resolvedPaths.extensions.filter((r) => r.enabled).map((r) => r.path);
+		const cliEnabledExtensions = cliExtensionPaths.extensions.filter((r) => r.enabled).map((r) => r.path);
+		const extensionPaths = this.noExtensions
+			? cliEnabledExtensions
+			: this.mergePaths(cliEnabledExtensions, enabledExtensions);
+		const extensionsResult = await loadExtensionsCached(extensionPaths, this.cwd, this.eventBus);
+		if (!options.includeInlineFactories) {
+			return extensionsResult;
+		}
+
+		const inlineExtensions = await this.loadExtensionFactories(extensionsResult.runtime);
+		extensionsResult.extensions.push(...inlineExtensions.extensions);
+		extensionsResult.errors.push(...inlineExtensions.errors);
+		return extensionsResult;
+	}
+
+	private resolveExtensionLoadPath(path: string): string {
+		return resolvePath(path, this.cwd, { normalizeUnicodeSpaces: true });
+	}
+
+	private async loadFinalExtensionSet(
+		extensionPaths: string[],
+		preTrustExtensions: LoadExtensionsResult | undefined,
+	): Promise<LoadExtensionsResult> {
+		if (!preTrustExtensions) {
+			const extensionsResult = await loadExtensionsCached(extensionPaths, this.cwd, this.eventBus);
+			const inlineExtensions = await this.loadExtensionFactories(extensionsResult.runtime);
+			extensionsResult.extensions.push(...inlineExtensions.extensions);
+			extensionsResult.errors.push(...inlineExtensions.errors);
+			this.addExtensionConflictDiagnostics(extensionsResult);
+			return extensionsResult;
+		}
+
+		const preloadedByPath = new Map(
+			preTrustExtensions.extensions
+				.filter((extension) => !extension.path.startsWith("<inline:"))
+				.map((extension) => [extension.resolvedPath, extension]),
+		);
+		const failedPreloadPaths = new Set(
+			preTrustExtensions.errors.map((error) => this.resolveExtensionLoadPath(error.path)),
+		);
+		const remainingPaths = extensionPaths.filter((path) => {
+			const resolvedPath = this.resolveExtensionLoadPath(path);
+			return !preloadedByPath.has(resolvedPath) && !failedPreloadPaths.has(resolvedPath);
+		});
+		const remainingExtensions = await loadExtensionsCached(
+			remainingPaths,
+			this.cwd,
+			this.eventBus,
+			preTrustExtensions.runtime,
+		);
+		const loadedByPath = new Map(preloadedByPath);
+		for (const extension of remainingExtensions.extensions) {
+			loadedByPath.set(extension.resolvedPath, extension);
+		}
+
+		const inlineExtensions = preTrustExtensions.extensions.filter((extension) =>
+			extension.path.startsWith("<inline:"),
+		);
+		const orderedExtensions = extensionPaths
+			.map((path) => loadedByPath.get(this.resolveExtensionLoadPath(path)))
+			.filter((extension): extension is Extension => extension !== undefined);
+		orderedExtensions.push(...inlineExtensions);
+
+		const extensionsResult: LoadExtensionsResult = {
+			extensions: orderedExtensions,
+			errors: [...preTrustExtensions.errors, ...remainingExtensions.errors],
+			runtime: preTrustExtensions.runtime,
+		};
+		this.addExtensionConflictDiagnostics(extensionsResult);
+		return extensionsResult;
+	}
+
+	private addExtensionConflictDiagnostics(extensionsResult: LoadExtensionsResult): void {
+		// Detect extension conflicts (tools, commands, flags with same names from different extensions)
+		// Keep all extensions loaded. Conflicts are reported as diagnostics, and precedence is handled by load order.
+		const conflicts = this.detectExtensionConflicts(extensionsResult.extensions);
+		for (const conflict of conflicts) {
+			extensionsResult.errors.push({ path: conflict.path, error: conflict.message });
+		}
+	}
+
+	private mapSkillPath(resource: ResolvedResource, metadataByPath: Map<string, PathMetadata>): string {
+		if (resource.metadata.source !== "auto" && resource.metadata.origin !== "package") {
+			return resource.path;
+		}
+		try {
+			const stats = statSync(resource.path);
+			if (!stats.isDirectory()) {
+				return resource.path;
+			}
+		} catch {
+			return resource.path;
+		}
+		const skillFile = join(resource.path, "SKILL.md");
+		if (existsSync(skillFile)) {
+			if (!metadataByPath.has(skillFile)) {
+				metadataByPath.set(skillFile, resource.metadata);
+			}
+			return skillFile;
+		}
+		return resource.path;
+	}
+
+	private normalizeExtensionPaths(
+		entries: Array<{ path: string; metadata: PathMetadata }>,
+	): Array<{ path: string; metadata: PathMetadata }> {
+		return entries.map((entry) => {
+			const metadata = entry.metadata.baseDir
+				? { ...entry.metadata, baseDir: this.resolveResourcePath(entry.metadata.baseDir) }
+				: entry.metadata;
+			return {
+				path: this.resolveResourcePath(entry.path),
+				metadata,
+			};
+		});
+	}
+
+	private updateSkillsFromPaths(skillPaths: string[], metadataByPath?: Map<string, PathMetadata>): void {
+		let skillsResult: { skills: Skill[]; diagnostics: ResourceDiagnostic[] };
+		if (this.noSkills && skillPaths.length === 0) {
+			skillsResult = { skills: [], diagnostics: [] };
+		} else {
+			skillsResult = loadSkills({
+				cwd: this.cwd,
+				agentDir: this.agentDir,
+				skillPaths,
+				includeDefaults: false,
+			});
+		}
+		const resolvedSkills = this.skillsOverride ? this.skillsOverride(skillsResult) : skillsResult;
+		this.skills = resolvedSkills.skills.map((skill) => ({
+			...skill,
+			sourceInfo:
+				this.findSourceInfoForPath(skill.filePath, this.extensionSkillSourceInfos, metadataByPath) ??
+				skill.sourceInfo ??
+				this.getDefaultSourceInfoForPath(skill.filePath),
+		}));
+		this.skillDiagnostics = resolvedSkills.diagnostics;
+	}
+
+	private updatePromptsFromPaths(promptPaths: string[], metadataByPath?: Map<string, PathMetadata>): void {
+		let promptsResult: { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] };
+		if (this.noPromptTemplates && promptPaths.length === 0) {
+			promptsResult = { prompts: [], diagnostics: [] };
+		} else {
+			const allPrompts = loadPromptTemplates({
+				cwd: this.cwd,
+				agentDir: this.agentDir,
+				promptPaths,
+				includeDefaults: false,
+			});
+			promptsResult = this.dedupePrompts(allPrompts);
+		}
+		const resolvedPrompts = this.promptsOverride ? this.promptsOverride(promptsResult) : promptsResult;
+		this.prompts = resolvedPrompts.prompts.map((prompt) => ({
+			...prompt,
+			sourceInfo:
+				this.findSourceInfoForPath(prompt.filePath, this.extensionPromptSourceInfos, metadataByPath) ??
+				prompt.sourceInfo ??
+				this.getDefaultSourceInfoForPath(prompt.filePath),
+		}));
+		this.promptDiagnostics = resolvedPrompts.diagnostics;
+	}
+
+	private updateThemesFromPaths(themePaths: string[], metadataByPath?: Map<string, PathMetadata>): void {
+		let themesResult: { themes: Theme[]; diagnostics: ResourceDiagnostic[] };
+		if (this.noThemes && themePaths.length === 0) {
+			themesResult = { themes: [], diagnostics: [] };
+		} else {
+			const loaded = this.loadThemes(themePaths, false);
+			const deduped = this.dedupeThemes(loaded.themes);
+			themesResult = { themes: deduped.themes, diagnostics: [...loaded.diagnostics, ...deduped.diagnostics] };
+		}
+		const resolvedThemes = this.themesOverride ? this.themesOverride(themesResult) : themesResult;
+		this.themes = resolvedThemes.themes.map((theme) => {
+			const sourcePath = theme.sourcePath;
+			theme.sourceInfo = sourcePath
+				? (this.findSourceInfoForPath(sourcePath, this.extensionThemeSourceInfos, metadataByPath) ??
+					theme.sourceInfo ??
+					this.getDefaultSourceInfoForPath(sourcePath))
+				: theme.sourceInfo;
+			return theme;
+		});
+		this.themeDiagnostics = resolvedThemes.diagnostics;
+	}
+
+	private applyExtensionSourceInfo(extensions: Extension[], metadataByPath: Map<string, PathMetadata>): void {
+		for (const extension of extensions) {
+			extension.sourceInfo =
+				this.findSourceInfoForPath(extension.path, undefined, metadataByPath) ??
+				this.getDefaultSourceInfoForPath(extension.path);
+			for (const command of extension.commands.values()) {
+				command.sourceInfo = extension.sourceInfo;
+			}
+			for (const tool of extension.tools.values()) {
+				tool.sourceInfo = extension.sourceInfo;
+			}
+		}
+	}
+
+	private findSourceInfoForPath(
+		resourcePath: string,
+		extraSourceInfos?: Map<string, SourceInfo>,
+		metadataByPath?: Map<string, PathMetadata>,
+	): SourceInfo | undefined {
+		if (!resourcePath) {
+			return undefined;
+		}
+
+		if (resourcePath.startsWith("<")) {
+			return this.getDefaultSourceInfoForPath(resourcePath);
+		}
+
+		const normalizedResourcePath = resolve(resourcePath);
+		if (extraSourceInfos) {
+			for (const [sourcePath, sourceInfo] of extraSourceInfos.entries()) {
+				const normalizedSourcePath = resolve(sourcePath);
+				if (
+					normalizedResourcePath === normalizedSourcePath ||
+					normalizedResourcePath.startsWith(`${normalizedSourcePath}${sep}`)
+				) {
+					return { ...sourceInfo, path: resourcePath };
+				}
+			}
+		}
+
+		if (metadataByPath) {
+			const exact = metadataByPath.get(normalizedResourcePath) ?? metadataByPath.get(resourcePath);
+			if (exact) {
+				return createSourceInfo(resourcePath, exact);
+			}
+
+			for (const [sourcePath, metadata] of metadataByPath.entries()) {
+				const normalizedSourcePath = resolve(sourcePath);
+				if (
+					normalizedResourcePath === normalizedSourcePath ||
+					normalizedResourcePath.startsWith(`${normalizedSourcePath}${sep}`)
+				) {
+					return createSourceInfo(resourcePath, metadata);
+				}
+			}
+		}
+
+		return undefined;
+	}
+
+	private getDefaultSourceInfoForPath(filePath: string): SourceInfo {
+		if (filePath.startsWith("<") && filePath.endsWith(">")) {
+			return {
+				path: filePath,
+				source: filePath.slice(1, -1).split(":")[0] || "temporary",
+				scope: "temporary",
+				origin: "top-level",
+			};
+		}
+
+		const normalizedPath = resolve(filePath);
+		const agentRoots = [
+			join(this.agentDir, "skills"),
+			join(this.agentDir, "prompts"),
+			join(this.agentDir, "themes"),
+			join(this.agentDir, "extensions"),
+		];
+		const projectRoots = [
+			join(this.cwd, CONFIG_DIR_NAME, "skills"),
+			join(this.cwd, CONFIG_DIR_NAME, "prompts"),
+			join(this.cwd, CONFIG_DIR_NAME, "themes"),
+			join(this.cwd, CONFIG_DIR_NAME, "extensions"),
+		];
+
+		for (const root of agentRoots) {
+			if (this.isUnderPath(normalizedPath, root)) {
+				return { path: filePath, source: "local", scope: "user", origin: "top-level", baseDir: root };
+			}
+		}
+
+		for (const root of projectRoots) {
+			if (this.isUnderPath(normalizedPath, root)) {
+				return { path: filePath, source: "local", scope: "project", origin: "top-level", baseDir: root };
+			}
+		}
+
+		return {
+			path: filePath,
+			source: "local",
+			scope: "temporary",
+			origin: "top-level",
+			baseDir: statSync(normalizedPath).isDirectory() ? normalizedPath : resolve(normalizedPath, ".."),
+		};
+	}
+
+	private mergePaths(primary: string[], additional: string[]): string[] {
+		const merged: string[] = [];
+		const seen = new Set<string>();
+
+		for (const p of [...primary, ...additional]) {
+			const resolved = this.resolveResourcePath(p);
+			const canonicalPath = canonicalizePath(resolved);
+			if (seen.has(canonicalPath)) continue;
+			seen.add(canonicalPath);
+			merged.push(resolved);
+		}
+
+		return merged;
+	}
+
+	private resolveResourcePath(p: string): string {
+		return resolvePath(p, this.cwd, { trim: true });
+	}
+
+	private loadThemes(
+		paths: string[],
+		includeDefaults: boolean = true,
+	): {
+		themes: Theme[];
+		diagnostics: ResourceDiagnostic[];
+	} {
+		const themes: Theme[] = [];
+		const diagnostics: ResourceDiagnostic[] = [];
+		if (includeDefaults) {
+			const defaultDirs = [join(this.agentDir, "themes"), join(this.cwd, CONFIG_DIR_NAME, "themes")];
+
+			for (const dir of defaultDirs) {
+				this.loadThemesFromDir(dir, themes, diagnostics);
+			}
+		}
+
+		for (const p of paths) {
+			const resolved = this.resolveResourcePath(p);
+			if (!existsSync(resolved)) {
+				diagnostics.push({ type: "warning", message: "theme path does not exist", path: resolved });
+				continue;
+			}
+
+			try {
+				const stats = statSync(resolved);
+				if (stats.isDirectory()) {
+					this.loadThemesFromDir(resolved, themes, diagnostics);
+				} else if (stats.isFile() && resolved.endsWith(".json")) {
+					this.loadThemeFromFile(resolved, themes, diagnostics);
+				} else {
+					diagnostics.push({ type: "warning", message: "theme path is not a json file", path: resolved });
+				}
+			} catch (error) {
+				const message = error instanceof Error ? error.message : "failed to read theme path";
+				diagnostics.push({ type: "warning", message, path: resolved });
+			}
+		}
+
+		return { themes, diagnostics };
+	}
+
+	private loadThemesFromDir(dir: string, themes: Theme[], diagnostics: ResourceDiagnostic[]): void {
+		if (!existsSync(dir)) {
+			return;
+		}
+
+		try {
+			const entries = readdirSync(dir, { withFileTypes: true });
+			for (const entry of entries) {
+				let isFile = entry.isFile();
+				if (entry.isSymbolicLink()) {
+					try {
+						isFile = statSync(join(dir, entry.name)).isFile();
+					} catch {
+						continue;
+					}
+				}
+				if (!isFile) {
+					continue;
+				}
+				if (!entry.name.endsWith(".json")) {
+					continue;
+				}
+				this.loadThemeFromFile(join(dir, entry.name), themes, diagnostics);
+			}
+		} catch (error) {
+			const message = error instanceof Error ? error.message : "failed to read theme directory";
+			diagnostics.push({ type: "warning", message, path: dir });
+		}
+	}
+
+	private loadThemeFromFile(filePath: string, themes: Theme[], diagnostics: ResourceDiagnostic[]): void {
+		try {
+			themes.push(loadThemeFromPath(filePath));
+		} catch (error) {
+			const message = error instanceof Error ? error.message : "failed to load theme";
+			diagnostics.push({ type: "warning", message, path: filePath });
+		}
+	}
+
+	private async loadExtensionFactories(runtime: ExtensionRuntime): Promise<{
+		extensions: Extension[];
+		errors: Array<{ path: string; error: string }>;
+	}> {
+		const extensions: Extension[] = [];
+		const errors: Array<{ path: string; error: string }> = [];
+
+		for (const [index, input] of this.extensionFactories.entries()) {
+			const isNamed = typeof input !== "function";
+			const factory = isNamed ? input.factory : input;
+			const extensionPath = `<inline:${isNamed ? input.name : index + 1}>`;
+			try {
+				const extension = await loadExtensionFromFactory(factory, this.cwd, this.eventBus, runtime, extensionPath);
+				extensions.push(extension);
+			} catch (error) {
+				const message = error instanceof Error ? error.message : "failed to load extension";
+				errors.push({ path: extensionPath, error: message });
+			}
+		}
+
+		return { extensions, errors };
+	}
+
+	private dedupePrompts(prompts: PromptTemplate[]): { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] } {
+		const seen = new Map<string, PromptTemplate>();
+		const diagnostics: ResourceDiagnostic[] = [];
+
+		for (const prompt of prompts) {
+			const existing = seen.get(prompt.name);
+			if (existing) {
+				diagnostics.push({
+					type: "collision",
+					message: `name "/${prompt.name}" collision`,
+					path: prompt.filePath,
+					collision: {
+						resourceType: "prompt",
+						name: prompt.name,
+						winnerPath: existing.filePath,
+						loserPath: prompt.filePath,
+					},
+				});
+			} else {
+				seen.set(prompt.name, prompt);
+			}
+		}
+
+		return { prompts: Array.from(seen.values()), diagnostics };
+	}
+
+	private dedupeThemes(themes: Theme[]): { themes: Theme[]; diagnostics: ResourceDiagnostic[] } {
+		const seen = new Map<string, Theme>();
+		const diagnostics: ResourceDiagnostic[] = [];
+
+		for (const t of themes) {
+			const name = t.name ?? "unnamed";
+			const existing = seen.get(name);
+			if (existing) {
+				diagnostics.push({
+					type: "collision",
+					message: `name "${name}" collision`,
+					path: t.sourcePath,
+					collision: {
+						resourceType: "theme",
+						name,
+						winnerPath: existing.sourcePath ?? "<builtin>",
+						loserPath: t.sourcePath ?? "<builtin>",
+					},
+				});
+			} else {
+				seen.set(name, t);
+			}
+		}
+
+		return { themes: Array.from(seen.values()), diagnostics };
+	}
+
+	private discoverSystemPromptFile(): string | undefined {
+		const projectPath = join(this.cwd, CONFIG_DIR_NAME, "SYSTEM.md");
+		if (this.settingsManager.isProjectTrusted() && existsSync(projectPath)) {
+			return projectPath;
+		}
+
+		const globalPath = join(this.agentDir, "SYSTEM.md");
+		if (existsSync(globalPath)) {
+			return globalPath;
+		}
+
+		return undefined;
+	}
+
+	private discoverAppendSystemPromptFile(): string | undefined {
+		const projectPath = join(this.cwd, CONFIG_DIR_NAME, "APPEND_SYSTEM.md");
+		if (this.settingsManager.isProjectTrusted() && existsSync(projectPath)) {
+			return projectPath;
+		}
+
+		const globalPath = join(this.agentDir, "APPEND_SYSTEM.md");
+		if (existsSync(globalPath)) {
+			return globalPath;
+		}
+
+		return undefined;
+	}
+
+	private isUnderPath(target: string, root: string): boolean {
+		const normalizedRoot = resolve(root);
+		if (target === normalizedRoot) {
+			return true;
+		}
+		const prefix = normalizedRoot.endsWith(sep) ? normalizedRoot : `${normalizedRoot}${sep}`;
+		return target.startsWith(prefix);
+	}
+
+	private detectExtensionConflicts(extensions: Extension[]): Array<{ path: string; message: string }> {
+		const conflicts: Array<{ path: string; message: string }> = [];
+
+		// Track which extension registered each tool and flag
+		const toolOwners = new Map<string, string>();
+		const flagOwners = new Map<string, string>();
+
+		for (const ext of extensions) {
+			// Check tools
+			for (const toolName of ext.tools.keys()) {
+				const existingOwner = toolOwners.get(toolName);
+				if (existingOwner && existingOwner !== ext.path) {
+					conflicts.push({
+						path: ext.path,
+						message: `Tool "${toolName}" conflicts with ${existingOwner}`,
+					});
+				} else {
+					toolOwners.set(toolName, ext.path);
+				}
+			}
+
+			// Check flags
+			for (const flagName of ext.flags.keys()) {
+				const existingOwner = flagOwners.get(flagName);
+				if (existingOwner && existingOwner !== ext.path) {
+					conflicts.push({
+						path: ext.path,
+						message: `Flag "--${flagName}" conflicts with ${existingOwner}`,
+					});
+				} else {
+					flagOwners.set(flagName, ext.path);
+				}
+			}
+		}
+
+		return conflicts;
+	}
+}