@earendil-works/pi-coding-agent 0.78.0 → 0.79.0

package/dist/core/resource-loader.js

@@ -54,23 +54,25 @@ export function loadProjectContextFiles(options) {
         contextFiles.push(globalContext);
         seenPaths.add(globalContext.path);
     }
-    const ancestorContextFiles = [];
-    let currentDir = resolvedCwd;
-    const root = resolve("/");
-    while (true) {
-        const contextFile = loadContextFileFromDir(currentDir);
-        if (contextFile && !seenPaths.has(contextFile.path)) {
-            ancestorContextFiles.unshift(contextFile);
-            seenPaths.add(contextFile.path);
-        }
-        if (currentDir === root)
-            break;
-        const parentDir = resolve(currentDir, "..");
-        if (parentDir === currentDir)
-            break;
-        currentDir = parentDir;
-    }
-    contextFiles.push(...ancestorContextFiles);
+    if (options.projectTrusted !== false) {
+        const ancestorContextFiles = [];
+        let currentDir = resolvedCwd;
+        const root = resolve("/");
+        while (true) {
+            const contextFile = loadContextFileFromDir(currentDir);
+            if (contextFile && !seenPaths.has(contextFile.path)) {
+                ancestorContextFiles.unshift(contextFile);
+                seenPaths.add(contextFile.path);
+            }
+            if (currentDir === root)
+                break;
+            const parentDir = resolve(currentDir, "..");
+            if (parentDir === currentDir)
+                break;
+            currentDir = parentDir;
+        }
+        contextFiles.push(...ancestorContextFiles);
+    }
     return contextFiles;
 }
 export class DefaultResourceLoader {
@@ -206,7 +208,18 @@ export class DefaultResourceLoader {
             this.updateThemesFromPaths(this.lastThemePaths);
         }
     }
-    async reload() {
+    async reload(options) {
+        let preTrustExtensions;
+        if (options?.resolveProjectTrust) {
+            // 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();
+            preTrustExtensions = await this.loadCurrentExtensionSet({ includeInlineFactories: true });
+            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, {
@@ -230,29 +243,7 @@ export class DefaultResourceLoader {
         const enabledSkillResources = getEnabledResources(resolvedPaths.skills);
         const enabledPrompts = getEnabledPaths(resolvedPaths.prompts);
         const enabledThemes = getEnabledPaths(resolvedPaths.themes);
-        const mapSkillPath = (resource) => {
-            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;
-        };
-        const enabledSkills = enabledSkillResources.map(mapSkillPath);
+        const enabledSkills = enabledSkillResources.map((resource) => this.mapSkillPath(resource, metadataByPath));
         // Add CLI paths metadata
         for (const r of cliExtensionPaths.extensions) {
             if (!metadataByPath.has(r.path)) {
@@ -271,16 +262,7 @@ export class DefaultResourceLoader {
         const extensionPaths = this.noExtensions
             ? cliEnabledExtensions
             : this.mergePaths(cliEnabledExtensions, enabledExtensions);
-        const extensionsResult = await loadExtensions(extensionPaths, this.cwd, this.eventBus);
-        const inlineExtensions = await this.loadExtensionFactories(extensionsResult.runtime);
-        extensionsResult.extensions.push(...inlineExtensions.extensions);
-        extensionsResult.errors.push(...inlineExtensions.errors);
-        // 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 });
-        }
+        const extensionsResult = await this.loadFinalExtensionSet(extensionPaths, preTrustExtensions);
         for (const p of this.additionalExtensionPaths) {
             if (isLocalPath(p)) {
                 const resolved = this.resolveResourcePath(p);
@@ -333,7 +315,13 @@ export class DefaultResourceLoader {
             }
         }
         const agentsFiles = {
-            agentsFiles: this.noContextFiles ? [] : loadProjectContextFiles({ cwd: this.cwd, agentDir: this.agentDir }),
+            agentsFiles: this.noContextFiles
+                ? []
+                : loadProjectContextFiles({
+                    cwd: this.cwd,
+                    agentDir: this.agentDir,
+                    projectTrusted: this.settingsManager.isProjectTrusted(),
+                }),
         };
         const resolvedAgentsFiles = this.agentsFilesOverride ? this.agentsFilesOverride(agentsFiles) : agentsFiles;
         this.agentsFiles = resolvedAgentsFiles.agentsFiles;
@@ -348,6 +336,93 @@ export class DefaultResourceLoader {
             ? this.appendSystemPromptOverride(baseAppend)
             : baseAppend;
     }
+    async loadCurrentExtensionSet(options) {
+        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 loadExtensions(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;
+    }
+    resolveExtensionLoadPath(path) {
+        return resolvePath(path, this.cwd, { normalizeUnicodeSpaces: true });
+    }
+    async loadFinalExtensionSet(extensionPaths, preTrustExtensions) {
+        if (!preTrustExtensions) {
+            const extensionsResult = await loadExtensions(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 loadExtensions(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 !== undefined);
+        orderedExtensions.push(...inlineExtensions);
+        const extensionsResult = {
+            extensions: orderedExtensions,
+            errors: [...preTrustExtensions.errors, ...remainingExtensions.errors],
+            runtime: preTrustExtensions.runtime,
+        };
+        this.addExtensionConflictDiagnostics(extensionsResult);
+        return extensionsResult;
+    }
+    addExtensionConflictDiagnostics(extensionsResult) {
+        // 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 });
+        }
+    }
+    mapSkillPath(resource, metadataByPath) {
+        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;
+    }
     normalizeExtensionPaths(entries) {
         return entries.map((entry) => {
             const metadata = entry.metadata.baseDir
@@ -667,7 +742,7 @@ export class DefaultResourceLoader {
     }
     discoverSystemPromptFile() {
         const projectPath = join(this.cwd, CONFIG_DIR_NAME, "SYSTEM.md");
-        if (existsSync(projectPath)) {
+        if (this.settingsManager.isProjectTrusted() && existsSync(projectPath)) {
             return projectPath;
         }
         const globalPath = join(this.agentDir, "SYSTEM.md");
@@ -678,7 +753,7 @@ export class DefaultResourceLoader {
     }
     discoverAppendSystemPromptFile() {
         const projectPath = join(this.cwd, CONFIG_DIR_NAME, "APPEND_SYSTEM.md");
-        if (existsSync(projectPath)) {
+        if (this.settingsManager.isProjectTrusted() && existsSync(projectPath)) {
             return projectPath;
         }
         const globalPath = join(this.agentDir, "APPEND_SYSTEM.md");

package/dist/core/resource-loader.js.map

@@ -1 +1 @@
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{ existsSync, readdirSync, readFileSync, statSync } from \"node:fs\";\nimport { join, resolve, sep } from \"node:path\";\nimport chalk from \"chalk\";\nimport { CONFIG_DIR_NAME } from \"../config.ts\";\nimport { loadThemeFromPath, type Theme } from \"../modes/interactive/theme/theme.ts\";\nimport type { ResourceDiagnostic } from \"./diagnostics.ts\";\n\nexport type { ResourceCollision, ResourceDiagnostic } from \"./diagnostics.ts\";\n\nimport { canonicalizePath, isLocalPath, resolvePath } from \"../utils/paths.ts\";\nimport { createEventBus, type EventBus } from \"./event-bus.ts\";\nimport { createExtensionRuntime, loadExtensionFromFactory, loadExtensions } from \"./extensions/loader.ts\";\nimport type { Extension, ExtensionFactory, ExtensionRuntime, LoadExtensionsResult } from \"./extensions/types.ts\";\nimport { DefaultPackageManager, type PathMetadata } from \"./package-manager.ts\";\nimport type { PromptTemplate } from \"./prompt-templates.ts\";\nimport { loadPromptTemplates } from \"./prompt-templates.ts\";\nimport { SettingsManager } from \"./settings-manager.ts\";\nimport type { Skill } from \"./skills.ts\";\nimport { loadSkills } from \"./skills.ts\";\nimport { createSourceInfo, type SourceInfo } from \"./source-info.ts\";\n\nexport interface ResourceExtensionPaths {\n\tskillPaths?: Array<{ path: string; metadata: PathMetadata }>;\n\tpromptPaths?: Array<{ path: string; metadata: PathMetadata }>;\n\tthemePaths?: Array<{ path: string; metadata: PathMetadata }>;\n}\n\nexport interface ResourceLoader {\n\tgetExtensions(): LoadExtensionsResult;\n\tgetSkills(): { skills: Skill[]; diagnostics: ResourceDiagnostic[] };\n\tgetPrompts(): { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] };\n\tgetThemes(): { themes: Theme[]; diagnostics: ResourceDiagnostic[] };\n\tgetAgentsFiles(): { agentsFiles: Array<{ path: string; content: string }> };\n\tgetSystemPrompt(): string | undefined;\n\tgetAppendSystemPrompt(): string[];\n\textendResources(paths: ResourceExtensionPaths): void;\n\treload(): Promise<void>;\n}\n\nfunction resolvePromptInput(input: string | undefined, description: string): string | undefined {\n\tif (!input) {\n\t\treturn undefined;\n\t}\n\n\tif (existsSync(input)) {\n\t\ttry {\n\t\t\treturn readFileSync(input, \"utf-8\");\n\t\t} catch (error) {\n\t\t\tconsole.error(chalk.yellow(`Warning: Could not read ${description} file ${input}: ${error}`));\n\t\t\treturn input;\n\t\t}\n\t}\n\n\treturn input;\n}\n\nfunction loadContextFileFromDir(dir: string): { path: string; content: string } | null {\n\tconst candidates = [\"AGENTS.md\", \"AGENTS.MD\", \"CLAUDE.md\", \"CLAUDE.MD\"];\n\tfor (const filename of candidates) {\n\t\tconst filePath = join(dir, filename);\n\t\tif (existsSync(filePath)) {\n\t\t\ttry {\n\t\t\t\treturn {\n\t\t\t\t\tpath: filePath,\n\t\t\t\t\tcontent: readFileSync(filePath, \"utf-8\"),\n\t\t\t\t};\n\t\t\t} catch (error) {\n\t\t\t\tconsole.error(chalk.yellow(`Warning: Could not read ${filePath}: ${error}`));\n\t\t\t}\n\t\t}\n\t}\n\treturn null;\n}\n\nexport function loadProjectContextFiles(options: {\n\tcwd: string;\n\tagentDir: string;\n}): Array<{ path: string; content: string }> {\n\tconst resolvedCwd = resolvePath(options.cwd);\n\tconst resolvedAgentDir = resolvePath(options.agentDir);\n\n\tconst contextFiles: Array<{ path: string; content: string }> = [];\n\tconst seenPaths = new Set<string>();\n\n\tconst globalContext = loadContextFileFromDir(resolvedAgentDir);\n\tif (globalContext) {\n\t\tcontextFiles.push(globalContext);\n\t\tseenPaths.add(globalContext.path);\n\t}\n\n\tconst ancestorContextFiles: Array<{ path: string; content: string }> = [];\n\n\tlet currentDir = resolvedCwd;\n\tconst root = resolve(\"/\");\n\n\twhile (true) {\n\t\tconst contextFile = loadContextFileFromDir(currentDir);\n\t\tif (contextFile && !seenPaths.has(contextFile.path)) {\n\t\t\tancestorContextFiles.unshift(contextFile);\n\t\t\tseenPaths.add(contextFile.path);\n\t\t}\n\n\t\tif (currentDir === root) break;\n\n\t\tconst parentDir = resolve(currentDir, \"..\");\n\t\tif (parentDir === currentDir) break;\n\t\tcurrentDir = parentDir;\n\t}\n\n\tcontextFiles.push(...ancestorContextFiles);\n\n\treturn contextFiles;\n}\n\nexport interface DefaultResourceLoaderOptions {\n\tcwd: string;\n\tagentDir: string;\n\tsettingsManager?: SettingsManager;\n\teventBus?: EventBus;\n\tadditionalExtensionPaths?: string[];\n\tadditionalSkillPaths?: string[];\n\tadditionalPromptTemplatePaths?: string[];\n\tadditionalThemePaths?: string[];\n\textensionFactories?: ExtensionFactory[];\n\tnoExtensions?: boolean;\n\tnoSkills?: boolean;\n\tnoPromptTemplates?: boolean;\n\tnoThemes?: boolean;\n\tnoContextFiles?: boolean;\n\tsystemPrompt?: string;\n\tappendSystemPrompt?: string[];\n\textensionsOverride?: (base: LoadExtensionsResult) => LoadExtensionsResult;\n\tskillsOverride?: (base: { skills: Skill[]; diagnostics: ResourceDiagnostic[] }) => {\n\t\tskills: Skill[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t};\n\tpromptsOverride?: (base: { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] }) => {\n\t\tprompts: PromptTemplate[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t};\n\tthemesOverride?: (base: { themes: Theme[]; diagnostics: ResourceDiagnostic[] }) => {\n\t\tthemes: Theme[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t};\n\tagentsFilesOverride?: (base: { agentsFiles: Array<{ path: string; content: string }> }) => {\n\t\tagentsFiles: Array<{ path: string; content: string }>;\n\t};\n\tsystemPromptOverride?: (base: string | undefined) => string | undefined;\n\tappendSystemPromptOverride?: (base: string[]) => string[];\n}\n\nexport class DefaultResourceLoader implements ResourceLoader {\n\tprivate cwd: string;\n\tprivate agentDir: string;\n\tprivate settingsManager: SettingsManager;\n\tprivate eventBus: EventBus;\n\tprivate packageManager: DefaultPackageManager;\n\tprivate additionalExtensionPaths: string[];\n\tprivate additionalSkillPaths: string[];\n\tprivate additionalPromptTemplatePaths: string[];\n\tprivate additionalThemePaths: string[];\n\tprivate extensionFactories: ExtensionFactory[];\n\tprivate noExtensions: boolean;\n\tprivate noSkills: boolean;\n\tprivate noPromptTemplates: boolean;\n\tprivate noThemes: boolean;\n\tprivate noContextFiles: boolean;\n\tprivate systemPromptSource?: string;\n\tprivate appendSystemPromptSource?: string[];\n\tprivate extensionsOverride?: (base: LoadExtensionsResult) => LoadExtensionsResult;\n\tprivate skillsOverride?: (base: { skills: Skill[]; diagnostics: ResourceDiagnostic[] }) => {\n\t\tskills: Skill[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t};\n\tprivate promptsOverride?: (base: { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] }) => {\n\t\tprompts: PromptTemplate[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t};\n\tprivate themesOverride?: (base: { themes: Theme[]; diagnostics: ResourceDiagnostic[] }) => {\n\t\tthemes: Theme[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t};\n\tprivate agentsFilesOverride?: (base: { agentsFiles: Array<{ path: string; content: string }> }) => {\n\t\tagentsFiles: Array<{ path: string; content: string }>;\n\t};\n\tprivate systemPromptOverride?: (base: string | undefined) => string | undefined;\n\tprivate appendSystemPromptOverride?: (base: string[]) => string[];\n\n\tprivate extensionsResult: LoadExtensionsResult;\n\tprivate skills: Skill[];\n\tprivate skillDiagnostics: ResourceDiagnostic[];\n\tprivate prompts: PromptTemplate[];\n\tprivate promptDiagnostics: ResourceDiagnostic[];\n\tprivate themes: Theme[];\n\tprivate themeDiagnostics: ResourceDiagnostic[];\n\tprivate agentsFiles: Array<{ path: string; content: string }>;\n\tprivate systemPrompt?: string;\n\tprivate appendSystemPrompt: string[];\n\tprivate lastSkillPaths: string[];\n\tprivate extensionSkillSourceInfos: Map<string, SourceInfo>;\n\tprivate extensionPromptSourceInfos: Map<string, SourceInfo>;\n\tprivate extensionThemeSourceInfos: Map<string, SourceInfo>;\n\tprivate lastPromptPaths: string[];\n\tprivate lastThemePaths: string[];\n\n\tconstructor(options: DefaultResourceLoaderOptions) {\n\t\tthis.cwd = resolvePath(options.cwd);\n\t\tthis.agentDir = resolvePath(options.agentDir);\n\t\tthis.settingsManager = options.settingsManager ?? SettingsManager.create(this.cwd, this.agentDir);\n\t\tthis.eventBus = options.eventBus ?? createEventBus();\n\t\tthis.packageManager = new DefaultPackageManager({\n\t\t\tcwd: this.cwd,\n\t\t\tagentDir: this.agentDir,\n\t\t\tsettingsManager: this.settingsManager,\n\t\t});\n\t\tthis.additionalExtensionPaths = options.additionalExtensionPaths ?? [];\n\t\tthis.additionalSkillPaths = options.additionalSkillPaths ?? [];\n\t\tthis.additionalPromptTemplatePaths = options.additionalPromptTemplatePaths ?? [];\n\t\tthis.additionalThemePaths = options.additionalThemePaths ?? [];\n\t\tthis.extensionFactories = options.extensionFactories ?? [];\n\t\tthis.noExtensions = options.noExtensions ?? false;\n\t\tthis.noSkills = options.noSkills ?? false;\n\t\tthis.noPromptTemplates = options.noPromptTemplates ?? false;\n\t\tthis.noThemes = options.noThemes ?? false;\n\t\tthis.noContextFiles = options.noContextFiles ?? false;\n\t\tthis.systemPromptSource = options.systemPrompt;\n\t\tthis.appendSystemPromptSource = options.appendSystemPrompt;\n\t\tthis.extensionsOverride = options.extensionsOverride;\n\t\tthis.skillsOverride = options.skillsOverride;\n\t\tthis.promptsOverride = options.promptsOverride;\n\t\tthis.themesOverride = options.themesOverride;\n\t\tthis.agentsFilesOverride = options.agentsFilesOverride;\n\t\tthis.systemPromptOverride = options.systemPromptOverride;\n\t\tthis.appendSystemPromptOverride = options.appendSystemPromptOverride;\n\n\t\tthis.extensionsResult = { extensions: [], errors: [], runtime: createExtensionRuntime() };\n\t\tthis.skills = [];\n\t\tthis.skillDiagnostics = [];\n\t\tthis.prompts = [];\n\t\tthis.promptDiagnostics = [];\n\t\tthis.themes = [];\n\t\tthis.themeDiagnostics = [];\n\t\tthis.agentsFiles = [];\n\t\tthis.appendSystemPrompt = [];\n\t\tthis.lastSkillPaths = [];\n\t\tthis.extensionSkillSourceInfos = new Map();\n\t\tthis.extensionPromptSourceInfos = new Map();\n\t\tthis.extensionThemeSourceInfos = new Map();\n\t\tthis.lastPromptPaths = [];\n\t\tthis.lastThemePaths = [];\n\t}\n\n\tgetExtensions(): LoadExtensionsResult {\n\t\treturn this.extensionsResult;\n\t}\n\n\tgetSkills(): { skills: Skill[]; diagnostics: ResourceDiagnostic[] } {\n\t\treturn { skills: this.skills, diagnostics: this.skillDiagnostics };\n\t}\n\n\tgetPrompts(): { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] } {\n\t\treturn { prompts: this.prompts, diagnostics: this.promptDiagnostics };\n\t}\n\n\tgetThemes(): { themes: Theme[]; diagnostics: ResourceDiagnostic[] } {\n\t\treturn { themes: this.themes, diagnostics: this.themeDiagnostics };\n\t}\n\n\tgetAgentsFiles(): { agentsFiles: Array<{ path: string; content: string }> } {\n\t\treturn { agentsFiles: this.agentsFiles };\n\t}\n\n\tgetSystemPrompt(): string | undefined {\n\t\treturn this.systemPrompt;\n\t}\n\n\tgetAppendSystemPrompt(): string[] {\n\t\treturn this.appendSystemPrompt;\n\t}\n\n\textendResources(paths: ResourceExtensionPaths): void {\n\t\tconst skillPaths = this.normalizeExtensionPaths(paths.skillPaths ?? []);\n\t\tconst promptPaths = this.normalizeExtensionPaths(paths.promptPaths ?? []);\n\t\tconst themePaths = this.normalizeExtensionPaths(paths.themePaths ?? []);\n\n\t\tfor (const entry of skillPaths) {\n\t\t\tthis.extensionSkillSourceInfos.set(entry.path, createSourceInfo(entry.path, entry.metadata));\n\t\t}\n\t\tfor (const entry of promptPaths) {\n\t\t\tthis.extensionPromptSourceInfos.set(entry.path, createSourceInfo(entry.path, entry.metadata));\n\t\t}\n\t\tfor (const entry of themePaths) {\n\t\t\tthis.extensionThemeSourceInfos.set(entry.path, createSourceInfo(entry.path, entry.metadata));\n\t\t}\n\n\t\tif (skillPaths.length > 0) {\n\t\t\tthis.lastSkillPaths = this.mergePaths(\n\t\t\t\tthis.lastSkillPaths,\n\t\t\t\tskillPaths.map((entry) => entry.path),\n\t\t\t);\n\t\t\tthis.updateSkillsFromPaths(this.lastSkillPaths);\n\t\t}\n\n\t\tif (promptPaths.length > 0) {\n\t\t\tthis.lastPromptPaths = this.mergePaths(\n\t\t\t\tthis.lastPromptPaths,\n\t\t\t\tpromptPaths.map((entry) => entry.path),\n\t\t\t);\n\t\t\tthis.updatePromptsFromPaths(this.lastPromptPaths);\n\t\t}\n\n\t\tif (themePaths.length > 0) {\n\t\t\tthis.lastThemePaths = this.mergePaths(\n\t\t\t\tthis.lastThemePaths,\n\t\t\t\tthemePaths.map((entry) => entry.path),\n\t\t\t);\n\t\t\tthis.updateThemesFromPaths(this.lastThemePaths);\n\t\t}\n\t}\n\n\tasync reload(): Promise<void> {\n\t\tawait this.settingsManager.reload();\n\t\tconst resolvedPaths = await this.packageManager.resolve();\n\t\tconst cliExtensionPaths = await this.packageManager.resolveExtensionSources(this.additionalExtensionPaths, {\n\t\t\ttemporary: true,\n\t\t});\n\t\tconst metadataByPath = new Map<string, PathMetadata>();\n\n\t\tthis.extensionSkillSourceInfos = new Map();\n\t\tthis.extensionPromptSourceInfos = new Map();\n\t\tthis.extensionThemeSourceInfos = new Map();\n\n\t\t// Helper to extract enabled paths and store metadata\n\t\tconst getEnabledResources = (\n\t\t\tresources: Array<{ path: string; enabled: boolean; metadata: PathMetadata }>,\n\t\t): Array<{ path: string; enabled: boolean; metadata: PathMetadata }> => {\n\t\t\tfor (const r of resources) {\n\t\t\t\tif (!metadataByPath.has(r.path)) {\n\t\t\t\t\tmetadataByPath.set(r.path, r.metadata);\n\t\t\t\t}\n\t\t\t}\n\t\t\treturn resources.filter((r) => r.enabled);\n\t\t};\n\n\t\tconst getEnabledPaths = (\n\t\t\tresources: Array<{ path: string; enabled: boolean; metadata: PathMetadata }>,\n\t\t): string[] => getEnabledResources(resources).map((r) => r.path);\n\t\tconst enabledExtensions = getEnabledPaths(resolvedPaths.extensions);\n\t\tconst enabledSkillResources = getEnabledResources(resolvedPaths.skills);\n\t\tconst enabledPrompts = getEnabledPaths(resolvedPaths.prompts);\n\t\tconst enabledThemes = getEnabledPaths(resolvedPaths.themes);\n\n\t\tconst mapSkillPath = (resource: { path: string; metadata: PathMetadata }): string => {\n\t\t\tif (resource.metadata.source !== \"auto\" && resource.metadata.origin !== \"package\") {\n\t\t\t\treturn resource.path;\n\t\t\t}\n\t\t\ttry {\n\t\t\t\tconst stats = statSync(resource.path);\n\t\t\t\tif (!stats.isDirectory()) {\n\t\t\t\t\treturn resource.path;\n\t\t\t\t}\n\t\t\t} catch {\n\t\t\t\treturn resource.path;\n\t\t\t}\n\t\t\tconst skillFile = join(resource.path, \"SKILL.md\");\n\t\t\tif (existsSync(skillFile)) {\n\t\t\t\tif (!metadataByPath.has(skillFile)) {\n\t\t\t\t\tmetadataByPath.set(skillFile, resource.metadata);\n\t\t\t\t}\n\t\t\t\treturn skillFile;\n\t\t\t}\n\t\t\treturn resource.path;\n\t\t};\n\n\t\tconst enabledSkills = enabledSkillResources.map(mapSkillPath);\n\n\t\t// Add CLI paths metadata\n\t\tfor (const r of cliExtensionPaths.extensions) {\n\t\t\tif (!metadataByPath.has(r.path)) {\n\t\t\t\tmetadataByPath.set(r.path, { source: \"cli\", scope: \"temporary\", origin: \"top-level\" });\n\t\t\t}\n\t\t}\n\t\tfor (const r of cliExtensionPaths.skills) {\n\t\t\tif (!metadataByPath.has(r.path)) {\n\t\t\t\tmetadataByPath.set(r.path, { source: \"cli\", scope: \"temporary\", origin: \"top-level\" });\n\t\t\t}\n\t\t}\n\n\t\tconst cliEnabledExtensions = getEnabledPaths(cliExtensionPaths.extensions);\n\t\tconst cliEnabledSkills = getEnabledPaths(cliExtensionPaths.skills);\n\t\tconst cliEnabledPrompts = getEnabledPaths(cliExtensionPaths.prompts);\n\t\tconst cliEnabledThemes = getEnabledPaths(cliExtensionPaths.themes);\n\n\t\tconst extensionPaths = this.noExtensions\n\t\t\t? cliEnabledExtensions\n\t\t\t: this.mergePaths(cliEnabledExtensions, enabledExtensions);\n\n\t\tconst extensionsResult = await loadExtensions(extensionPaths, this.cwd, this.eventBus);\n\t\tconst inlineExtensions = await this.loadExtensionFactories(extensionsResult.runtime);\n\t\textensionsResult.extensions.push(...inlineExtensions.extensions);\n\t\textensionsResult.errors.push(...inlineExtensions.errors);\n\n\t\t// Detect extension conflicts (tools, commands, flags with same names from different extensions)\n\t\t// Keep all extensions loaded. Conflicts are reported as diagnostics, and precedence is handled by load order.\n\t\tconst conflicts = this.detectExtensionConflicts(extensionsResult.extensions);\n\t\tfor (const conflict of conflicts) {\n\t\t\textensionsResult.errors.push({ path: conflict.path, error: conflict.message });\n\t\t}\n\n\t\tfor (const p of this.additionalExtensionPaths) {\n\t\t\tif (isLocalPath(p)) {\n\t\t\t\tconst resolved = this.resolveResourcePath(p);\n\t\t\t\tif (!existsSync(resolved)) {\n\t\t\t\t\textensionsResult.errors.push({ path: resolved, error: `Extension path does not exist: ${resolved}` });\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tthis.extensionsResult = this.extensionsOverride ? this.extensionsOverride(extensionsResult) : extensionsResult;\n\t\tthis.applyExtensionSourceInfo(this.extensionsResult.extensions, metadataByPath);\n\n\t\tconst skillPaths = this.noSkills\n\t\t\t? this.mergePaths(cliEnabledSkills, this.additionalSkillPaths)\n\t\t\t: this.mergePaths([...cliEnabledSkills, ...enabledSkills], this.additionalSkillPaths);\n\n\t\tthis.lastSkillPaths = skillPaths;\n\t\tthis.updateSkillsFromPaths(skillPaths, metadataByPath);\n\t\tfor (const p of this.additionalSkillPaths) {\n\t\t\tif (isLocalPath(p)) {\n\t\t\t\tconst resolved = this.resolveResourcePath(p);\n\t\t\t\tif (!existsSync(resolved) && !this.skillDiagnostics.some((d) => d.path === resolved)) {\n\t\t\t\t\tthis.skillDiagnostics.push({ type: \"error\", message: \"Skill path does not exist\", path: resolved });\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tconst promptPaths = this.noPromptTemplates\n\t\t\t? this.mergePaths(cliEnabledPrompts, this.additionalPromptTemplatePaths)\n\t\t\t: this.mergePaths([...cliEnabledPrompts, ...enabledPrompts], this.additionalPromptTemplatePaths);\n\n\t\tthis.lastPromptPaths = promptPaths;\n\t\tthis.updatePromptsFromPaths(promptPaths, metadataByPath);\n\t\tfor (const p of this.additionalPromptTemplatePaths) {\n\t\t\tif (isLocalPath(p)) {\n\t\t\t\tconst resolved = this.resolveResourcePath(p);\n\t\t\t\tif (!existsSync(resolved) && !this.promptDiagnostics.some((d) => d.path === resolved)) {\n\t\t\t\t\tthis.promptDiagnostics.push({\n\t\t\t\t\t\ttype: \"error\",\n\t\t\t\t\t\tmessage: \"Prompt template path does not exist\",\n\t\t\t\t\t\tpath: resolved,\n\t\t\t\t\t});\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tconst themePaths = this.noThemes\n\t\t\t? this.mergePaths(cliEnabledThemes, this.additionalThemePaths)\n\t\t\t: this.mergePaths([...cliEnabledThemes, ...enabledThemes], this.additionalThemePaths);\n\n\t\tthis.lastThemePaths = themePaths;\n\t\tthis.updateThemesFromPaths(themePaths, metadataByPath);\n\t\tfor (const p of this.additionalThemePaths) {\n\t\t\tconst resolved = this.resolveResourcePath(p);\n\t\t\tif (!existsSync(resolved) && !this.themeDiagnostics.some((d) => d.path === resolved)) {\n\t\t\t\tthis.themeDiagnostics.push({ type: \"error\", message: \"Theme path does not exist\", path: resolved });\n\t\t\t}\n\t\t}\n\n\t\tconst agentsFiles = {\n\t\t\tagentsFiles: this.noContextFiles ? [] : loadProjectContextFiles({ cwd: this.cwd, agentDir: this.agentDir }),\n\t\t};\n\t\tconst resolvedAgentsFiles = this.agentsFilesOverride ? this.agentsFilesOverride(agentsFiles) : agentsFiles;\n\t\tthis.agentsFiles = resolvedAgentsFiles.agentsFiles;\n\n\t\tconst baseSystemPrompt = resolvePromptInput(\n\t\t\tthis.systemPromptSource ?? this.discoverSystemPromptFile(),\n\t\t\t\"system prompt\",\n\t\t);\n\t\tthis.systemPrompt = this.systemPromptOverride ? this.systemPromptOverride(baseSystemPrompt) : baseSystemPrompt;\n\n\t\tconst appendSources =\n\t\t\tthis.appendSystemPromptSource ??\n\t\t\t(this.discoverAppendSystemPromptFile() ? [this.discoverAppendSystemPromptFile()!] : []);\n\t\tconst baseAppend = appendSources\n\t\t\t.map((s) => resolvePromptInput(s, \"append system prompt\"))\n\t\t\t.filter((s): s is string => s !== undefined);\n\t\tthis.appendSystemPrompt = this.appendSystemPromptOverride\n\t\t\t? this.appendSystemPromptOverride(baseAppend)\n\t\t\t: baseAppend;\n\t}\n\n\tprivate normalizeExtensionPaths(\n\t\tentries: Array<{ path: string; metadata: PathMetadata }>,\n\t): Array<{ path: string; metadata: PathMetadata }> {\n\t\treturn entries.map((entry) => {\n\t\t\tconst metadata = entry.metadata.baseDir\n\t\t\t\t? { ...entry.metadata, baseDir: this.resolveResourcePath(entry.metadata.baseDir) }\n\t\t\t\t: entry.metadata;\n\t\t\treturn {\n\t\t\t\tpath: this.resolveResourcePath(entry.path),\n\t\t\t\tmetadata,\n\t\t\t};\n\t\t});\n\t}\n\n\tprivate updateSkillsFromPaths(skillPaths: string[], metadataByPath?: Map<string, PathMetadata>): void {\n\t\tlet skillsResult: { skills: Skill[]; diagnostics: ResourceDiagnostic[] };\n\t\tif (this.noSkills && skillPaths.length === 0) {\n\t\t\tskillsResult = { skills: [], diagnostics: [] };\n\t\t} else {\n\t\t\tskillsResult = loadSkills({\n\t\t\t\tcwd: this.cwd,\n\t\t\t\tagentDir: this.agentDir,\n\t\t\t\tskillPaths,\n\t\t\t\tincludeDefaults: false,\n\t\t\t});\n\t\t}\n\t\tconst resolvedSkills = this.skillsOverride ? this.skillsOverride(skillsResult) : skillsResult;\n\t\tthis.skills = resolvedSkills.skills.map((skill) => ({\n\t\t\t...skill,\n\t\t\tsourceInfo:\n\t\t\t\tthis.findSourceInfoForPath(skill.filePath, this.extensionSkillSourceInfos, metadataByPath) ??\n\t\t\t\tskill.sourceInfo ??\n\t\t\t\tthis.getDefaultSourceInfoForPath(skill.filePath),\n\t\t}));\n\t\tthis.skillDiagnostics = resolvedSkills.diagnostics;\n\t}\n\n\tprivate updatePromptsFromPaths(promptPaths: string[], metadataByPath?: Map<string, PathMetadata>): void {\n\t\tlet promptsResult: { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] };\n\t\tif (this.noPromptTemplates && promptPaths.length === 0) {\n\t\t\tpromptsResult = { prompts: [], diagnostics: [] };\n\t\t} else {\n\t\t\tconst allPrompts = loadPromptTemplates({\n\t\t\t\tcwd: this.cwd,\n\t\t\t\tagentDir: this.agentDir,\n\t\t\t\tpromptPaths,\n\t\t\t\tincludeDefaults: false,\n\t\t\t});\n\t\t\tpromptsResult = this.dedupePrompts(allPrompts);\n\t\t}\n\t\tconst resolvedPrompts = this.promptsOverride ? this.promptsOverride(promptsResult) : promptsResult;\n\t\tthis.prompts = resolvedPrompts.prompts.map((prompt) => ({\n\t\t\t...prompt,\n\t\t\tsourceInfo:\n\t\t\t\tthis.findSourceInfoForPath(prompt.filePath, this.extensionPromptSourceInfos, metadataByPath) ??\n\t\t\t\tprompt.sourceInfo ??\n\t\t\t\tthis.getDefaultSourceInfoForPath(prompt.filePath),\n\t\t}));\n\t\tthis.promptDiagnostics = resolvedPrompts.diagnostics;\n\t}\n\n\tprivate updateThemesFromPaths(themePaths: string[], metadataByPath?: Map<string, PathMetadata>): void {\n\t\tlet themesResult: { themes: Theme[]; diagnostics: ResourceDiagnostic[] };\n\t\tif (this.noThemes && themePaths.length === 0) {\n\t\t\tthemesResult = { themes: [], diagnostics: [] };\n\t\t} else {\n\t\t\tconst loaded = this.loadThemes(themePaths, false);\n\t\t\tconst deduped = this.dedupeThemes(loaded.themes);\n\t\t\tthemesResult = { themes: deduped.themes, diagnostics: [...loaded.diagnostics, ...deduped.diagnostics] };\n\t\t}\n\t\tconst resolvedThemes = this.themesOverride ? this.themesOverride(themesResult) : themesResult;\n\t\tthis.themes = resolvedThemes.themes.map((theme) => {\n\t\t\tconst sourcePath = theme.sourcePath;\n\t\t\ttheme.sourceInfo = sourcePath\n\t\t\t\t? (this.findSourceInfoForPath(sourcePath, this.extensionThemeSourceInfos, metadataByPath) ??\n\t\t\t\t\ttheme.sourceInfo ??\n\t\t\t\t\tthis.getDefaultSourceInfoForPath(sourcePath))\n\t\t\t\t: theme.sourceInfo;\n\t\t\treturn theme;\n\t\t});\n\t\tthis.themeDiagnostics = resolvedThemes.diagnostics;\n\t}\n\n\tprivate applyExtensionSourceInfo(extensions: Extension[], metadataByPath: Map<string, PathMetadata>): void {\n\t\tfor (const extension of extensions) {\n\t\t\textension.sourceInfo =\n\t\t\t\tthis.findSourceInfoForPath(extension.path, undefined, metadataByPath) ??\n\t\t\t\tthis.getDefaultSourceInfoForPath(extension.path);\n\t\t\tfor (const command of extension.commands.values()) {\n\t\t\t\tcommand.sourceInfo = extension.sourceInfo;\n\t\t\t}\n\t\t\tfor (const tool of extension.tools.values()) {\n\t\t\t\ttool.sourceInfo = extension.sourceInfo;\n\t\t\t}\n\t\t}\n\t}\n\n\tprivate findSourceInfoForPath(\n\t\tresourcePath: string,\n\t\textraSourceInfos?: Map<string, SourceInfo>,\n\t\tmetadataByPath?: Map<string, PathMetadata>,\n\t): SourceInfo | undefined {\n\t\tif (!resourcePath) {\n\t\t\treturn undefined;\n\t\t}\n\n\t\tif (resourcePath.startsWith(\"<\")) {\n\t\t\treturn this.getDefaultSourceInfoForPath(resourcePath);\n\t\t}\n\n\t\tconst normalizedResourcePath = resolve(resourcePath);\n\t\tif (extraSourceInfos) {\n\t\t\tfor (const [sourcePath, sourceInfo] of extraSourceInfos.entries()) {\n\t\t\t\tconst normalizedSourcePath = resolve(sourcePath);\n\t\t\t\tif (\n\t\t\t\t\tnormalizedResourcePath === normalizedSourcePath ||\n\t\t\t\t\tnormalizedResourcePath.startsWith(`${normalizedSourcePath}${sep}`)\n\t\t\t\t) {\n\t\t\t\t\treturn { ...sourceInfo, path: resourcePath };\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tif (metadataByPath) {\n\t\t\tconst exact = metadataByPath.get(normalizedResourcePath) ?? metadataByPath.get(resourcePath);\n\t\t\tif (exact) {\n\t\t\t\treturn createSourceInfo(resourcePath, exact);\n\t\t\t}\n\n\t\t\tfor (const [sourcePath, metadata] of metadataByPath.entries()) {\n\t\t\t\tconst normalizedSourcePath = resolve(sourcePath);\n\t\t\t\tif (\n\t\t\t\t\tnormalizedResourcePath === normalizedSourcePath ||\n\t\t\t\t\tnormalizedResourcePath.startsWith(`${normalizedSourcePath}${sep}`)\n\t\t\t\t) {\n\t\t\t\t\treturn createSourceInfo(resourcePath, metadata);\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\treturn undefined;\n\t}\n\n\tprivate getDefaultSourceInfoForPath(filePath: string): SourceInfo {\n\t\tif (filePath.startsWith(\"<\") && filePath.endsWith(\">\")) {\n\t\t\treturn {\n\t\t\t\tpath: filePath,\n\t\t\t\tsource: filePath.slice(1, -1).split(\":\")[0] || \"temporary\",\n\t\t\t\tscope: \"temporary\",\n\t\t\t\torigin: \"top-level\",\n\t\t\t};\n\t\t}\n\n\t\tconst normalizedPath = resolve(filePath);\n\t\tconst agentRoots = [\n\t\t\tjoin(this.agentDir, \"skills\"),\n\t\t\tjoin(this.agentDir, \"prompts\"),\n\t\t\tjoin(this.agentDir, \"themes\"),\n\t\t\tjoin(this.agentDir, \"extensions\"),\n\t\t];\n\t\tconst projectRoots = [\n\t\t\tjoin(this.cwd, CONFIG_DIR_NAME, \"skills\"),\n\t\t\tjoin(this.cwd, CONFIG_DIR_NAME, \"prompts\"),\n\t\t\tjoin(this.cwd, CONFIG_DIR_NAME, \"themes\"),\n\t\t\tjoin(this.cwd, CONFIG_DIR_NAME, \"extensions\"),\n\t\t];\n\n\t\tfor (const root of agentRoots) {\n\t\t\tif (this.isUnderPath(normalizedPath, root)) {\n\t\t\t\treturn { path: filePath, source: \"local\", scope: \"user\", origin: \"top-level\", baseDir: root };\n\t\t\t}\n\t\t}\n\n\t\tfor (const root of projectRoots) {\n\t\t\tif (this.isUnderPath(normalizedPath, root)) {\n\t\t\t\treturn { path: filePath, source: \"local\", scope: \"project\", origin: \"top-level\", baseDir: root };\n\t\t\t}\n\t\t}\n\n\t\treturn {\n\t\t\tpath: filePath,\n\t\t\tsource: \"local\",\n\t\t\tscope: \"temporary\",\n\t\t\torigin: \"top-level\",\n\t\t\tbaseDir: statSync(normalizedPath).isDirectory() ? normalizedPath : resolve(normalizedPath, \"..\"),\n\t\t};\n\t}\n\n\tprivate mergePaths(primary: string[], additional: string[]): string[] {\n\t\tconst merged: string[] = [];\n\t\tconst seen = new Set<string>();\n\n\t\tfor (const p of [...primary, ...additional]) {\n\t\t\tconst resolved = this.resolveResourcePath(p);\n\t\t\tconst canonicalPath = canonicalizePath(resolved);\n\t\t\tif (seen.has(canonicalPath)) continue;\n\t\t\tseen.add(canonicalPath);\n\t\t\tmerged.push(resolved);\n\t\t}\n\n\t\treturn merged;\n\t}\n\n\tprivate resolveResourcePath(p: string): string {\n\t\treturn resolvePath(p, this.cwd, { trim: true });\n\t}\n\n\tprivate loadThemes(\n\t\tpaths: string[],\n\t\tincludeDefaults: boolean = true,\n\t): {\n\t\tthemes: Theme[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t} {\n\t\tconst themes: Theme[] = [];\n\t\tconst diagnostics: ResourceDiagnostic[] = [];\n\t\tif (includeDefaults) {\n\t\t\tconst defaultDirs = [join(this.agentDir, \"themes\"), join(this.cwd, CONFIG_DIR_NAME, \"themes\")];\n\n\t\t\tfor (const dir of defaultDirs) {\n\t\t\t\tthis.loadThemesFromDir(dir, themes, diagnostics);\n\t\t\t}\n\t\t}\n\n\t\tfor (const p of paths) {\n\t\t\tconst resolved = this.resolveResourcePath(p);\n\t\t\tif (!existsSync(resolved)) {\n\t\t\t\tdiagnostics.push({ type: \"warning\", message: \"theme path does not exist\", path: resolved });\n\t\t\t\tcontinue;\n\t\t\t}\n\n\t\t\ttry {\n\t\t\t\tconst stats = statSync(resolved);\n\t\t\t\tif (stats.isDirectory()) {\n\t\t\t\t\tthis.loadThemesFromDir(resolved, themes, diagnostics);\n\t\t\t\t} else if (stats.isFile() && resolved.endsWith(\".json\")) {\n\t\t\t\t\tthis.loadThemeFromFile(resolved, themes, diagnostics);\n\t\t\t\t} else {\n\t\t\t\t\tdiagnostics.push({ type: \"warning\", message: \"theme path is not a json file\", path: resolved });\n\t\t\t\t}\n\t\t\t} catch (error) {\n\t\t\t\tconst message = error instanceof Error ? error.message : \"failed to read theme path\";\n\t\t\t\tdiagnostics.push({ type: \"warning\", message, path: resolved });\n\t\t\t}\n\t\t}\n\n\t\treturn { themes, diagnostics };\n\t}\n\n\tprivate loadThemesFromDir(dir: string, themes: Theme[], diagnostics: ResourceDiagnostic[]): void {\n\t\tif (!existsSync(dir)) {\n\t\t\treturn;\n\t\t}\n\n\t\ttry {\n\t\t\tconst entries = readdirSync(dir, { withFileTypes: true });\n\t\t\tfor (const entry of entries) {\n\t\t\t\tlet isFile = entry.isFile();\n\t\t\t\tif (entry.isSymbolicLink()) {\n\t\t\t\t\ttry {\n\t\t\t\t\t\tisFile = statSync(join(dir, entry.name)).isFile();\n\t\t\t\t\t} catch {\n\t\t\t\t\t\tcontinue;\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (!isFile) {\n\t\t\t\t\tcontinue;\n\t\t\t\t}\n\t\t\t\tif (!entry.name.endsWith(\".json\")) {\n\t\t\t\t\tcontinue;\n\t\t\t\t}\n\t\t\t\tthis.loadThemeFromFile(join(dir, entry.name), themes, diagnostics);\n\t\t\t}\n\t\t} catch (error) {\n\t\t\tconst message = error instanceof Error ? error.message : \"failed to read theme directory\";\n\t\t\tdiagnostics.push({ type: \"warning\", message, path: dir });\n\t\t}\n\t}\n\n\tprivate loadThemeFromFile(filePath: string, themes: Theme[], diagnostics: ResourceDiagnostic[]): void {\n\t\ttry {\n\t\t\tthemes.push(loadThemeFromPath(filePath));\n\t\t} catch (error) {\n\t\t\tconst message = error instanceof Error ? error.message : \"failed to load theme\";\n\t\t\tdiagnostics.push({ type: \"warning\", message, path: filePath });\n\t\t}\n\t}\n\n\tprivate async loadExtensionFactories(runtime: ExtensionRuntime): Promise<{\n\t\textensions: Extension[];\n\t\terrors: Array<{ path: string; error: string }>;\n\t}> {\n\t\tconst extensions: Extension[] = [];\n\t\tconst errors: Array<{ path: string; error: string }> = [];\n\n\t\tfor (const [index, factory] of this.extensionFactories.entries()) {\n\t\t\tconst extensionPath = `<inline:${index + 1}>`;\n\t\t\ttry {\n\t\t\t\tconst extension = await loadExtensionFromFactory(factory, this.cwd, this.eventBus, runtime, extensionPath);\n\t\t\t\textensions.push(extension);\n\t\t\t} catch (error) {\n\t\t\t\tconst message = error instanceof Error ? error.message : \"failed to load extension\";\n\t\t\t\terrors.push({ path: extensionPath, error: message });\n\t\t\t}\n\t\t}\n\n\t\treturn { extensions, errors };\n\t}\n\n\tprivate dedupePrompts(prompts: PromptTemplate[]): { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] } {\n\t\tconst seen = new Map<string, PromptTemplate>();\n\t\tconst diagnostics: ResourceDiagnostic[] = [];\n\n\t\tfor (const prompt of prompts) {\n\t\t\tconst existing = seen.get(prompt.name);\n\t\t\tif (existing) {\n\t\t\t\tdiagnostics.push({\n\t\t\t\t\ttype: \"collision\",\n\t\t\t\t\tmessage: `name \"/${prompt.name}\" collision`,\n\t\t\t\t\tpath: prompt.filePath,\n\t\t\t\t\tcollision: {\n\t\t\t\t\t\tresourceType: \"prompt\",\n\t\t\t\t\t\tname: prompt.name,\n\t\t\t\t\t\twinnerPath: existing.filePath,\n\t\t\t\t\t\tloserPath: prompt.filePath,\n\t\t\t\t\t},\n\t\t\t\t});\n\t\t\t} else {\n\t\t\t\tseen.set(prompt.name, prompt);\n\t\t\t}\n\t\t}\n\n\t\treturn { prompts: Array.from(seen.values()), diagnostics };\n\t}\n\n\tprivate dedupeThemes(themes: Theme[]): { themes: Theme[]; diagnostics: ResourceDiagnostic[] } {\n\t\tconst seen = new Map<string, Theme>();\n\t\tconst diagnostics: ResourceDiagnostic[] = [];\n\n\t\tfor (const t of themes) {\n\t\t\tconst name = t.name ?? \"unnamed\";\n\t\t\tconst existing = seen.get(name);\n\t\t\tif (existing) {\n\t\t\t\tdiagnostics.push({\n\t\t\t\t\ttype: \"collision\",\n\t\t\t\t\tmessage: `name \"${name}\" collision`,\n\t\t\t\t\tpath: t.sourcePath,\n\t\t\t\t\tcollision: {\n\t\t\t\t\t\tresourceType: \"theme\",\n\t\t\t\t\t\tname,\n\t\t\t\t\t\twinnerPath: existing.sourcePath ?? \"<builtin>\",\n\t\t\t\t\t\tloserPath: t.sourcePath ?? \"<builtin>\",\n\t\t\t\t\t},\n\t\t\t\t});\n\t\t\t} else {\n\t\t\t\tseen.set(name, t);\n\t\t\t}\n\t\t}\n\n\t\treturn { themes: Array.from(seen.values()), diagnostics };\n\t}\n\n\tprivate discoverSystemPromptFile(): string | undefined {\n\t\tconst projectPath = join(this.cwd, CONFIG_DIR_NAME, \"SYSTEM.md\");\n\t\tif (existsSync(projectPath)) {\n\t\t\treturn projectPath;\n\t\t}\n\n\t\tconst globalPath = join(this.agentDir, \"SYSTEM.md\");\n\t\tif (existsSync(globalPath)) {\n\t\t\treturn globalPath;\n\t\t}\n\n\t\treturn undefined;\n\t}\n\n\tprivate discoverAppendSystemPromptFile(): string | undefined {\n\t\tconst projectPath = join(this.cwd, CONFIG_DIR_NAME, \"APPEND_SYSTEM.md\");\n\t\tif (existsSync(projectPath)) {\n\t\t\treturn projectPath;\n\t\t}\n\n\t\tconst globalPath = join(this.agentDir, \"APPEND_SYSTEM.md\");\n\t\tif (existsSync(globalPath)) {\n\t\t\treturn globalPath;\n\t\t}\n\n\t\treturn undefined;\n\t}\n\n\tprivate isUnderPath(target: string, root: string): boolean {\n\t\tconst normalizedRoot = resolve(root);\n\t\tif (target === normalizedRoot) {\n\t\t\treturn true;\n\t\t}\n\t\tconst prefix = normalizedRoot.endsWith(sep) ? normalizedRoot : `${normalizedRoot}${sep}`;\n\t\treturn target.startsWith(prefix);\n\t}\n\n\tprivate detectExtensionConflicts(extensions: Extension[]): Array<{ path: string; message: string }> {\n\t\tconst conflicts: Array<{ path: string; message: string }> = [];\n\n\t\t// Track which extension registered each tool and flag\n\t\tconst toolOwners = new Map<string, string>();\n\t\tconst flagOwners = new Map<string, string>();\n\n\t\tfor (const ext of extensions) {\n\t\t\t// Check tools\n\t\t\tfor (const toolName of ext.tools.keys()) {\n\t\t\t\tconst existingOwner = toolOwners.get(toolName);\n\t\t\t\tif (existingOwner && existingOwner !== ext.path) {\n\t\t\t\t\tconflicts.push({\n\t\t\t\t\t\tpath: ext.path,\n\t\t\t\t\t\tmessage: `Tool \"${toolName}\" conflicts with ${existingOwner}`,\n\t\t\t\t\t});\n\t\t\t\t} else {\n\t\t\t\t\ttoolOwners.set(toolName, ext.path);\n\t\t\t\t}\n\t\t\t}\n\n\t\t\t// Check flags\n\t\t\tfor (const flagName of ext.flags.keys()) {\n\t\t\t\tconst existingOwner = flagOwners.get(flagName);\n\t\t\t\tif (existingOwner && existingOwner !== ext.path) {\n\t\t\t\t\tconflicts.push({\n\t\t\t\t\t\tpath: ext.path,\n\t\t\t\t\t\tmessage: `Flag \"--${flagName}\" conflicts with ${existingOwner}`,\n\t\t\t\t\t});\n\t\t\t\t} else {\n\t\t\t\t\tflagOwners.set(flagName, ext.path);\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\treturn conflicts;\n\t}\n}\n"]}
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{ existsSync, readdirSync, readFileSync, statSync } from \"node:fs\";\nimport { join, resolve, sep } from \"node:path\";\nimport chalk from \"chalk\";\nimport { CONFIG_DIR_NAME } from \"../config.ts\";\nimport { loadThemeFromPath, type Theme } from \"../modes/interactive/theme/theme.ts\";\nimport type { ResourceDiagnostic } from \"./diagnostics.ts\";\n\nexport type { ResourceCollision, ResourceDiagnostic } from \"./diagnostics.ts\";\n\nimport { canonicalizePath, isLocalPath, resolvePath } from \"../utils/paths.ts\";\nimport { createEventBus, type EventBus } from \"./event-bus.ts\";\nimport { createExtensionRuntime, loadExtensionFromFactory, loadExtensions } from \"./extensions/loader.ts\";\nimport type { Extension, ExtensionFactory, ExtensionRuntime, LoadExtensionsResult } from \"./extensions/types.ts\";\nimport { DefaultPackageManager, type PathMetadata, type ResolvedResource } from \"./package-manager.ts\";\nimport type { PromptTemplate } from \"./prompt-templates.ts\";\nimport { loadPromptTemplates } from \"./prompt-templates.ts\";\nimport { SettingsManager } from \"./settings-manager.ts\";\nimport type { Skill } from \"./skills.ts\";\nimport { loadSkills } from \"./skills.ts\";\nimport { createSourceInfo, type SourceInfo } from \"./source-info.ts\";\n\nexport interface ResourceExtensionPaths {\n\tskillPaths?: Array<{ path: string; metadata: PathMetadata }>;\n\tpromptPaths?: Array<{ path: string; metadata: PathMetadata }>;\n\tthemePaths?: Array<{ path: string; metadata: PathMetadata }>;\n}\n\nexport interface ResourceLoaderReloadOptions {\n\tresolveProjectTrust?: (input: { extensionsResult: LoadExtensionsResult }) => Promise<boolean>;\n}\n\nexport interface ResourceLoader {\n\tgetExtensions(): LoadExtensionsResult;\n\tgetSkills(): { skills: Skill[]; diagnostics: ResourceDiagnostic[] };\n\tgetPrompts(): { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] };\n\tgetThemes(): { themes: Theme[]; diagnostics: ResourceDiagnostic[] };\n\tgetAgentsFiles(): { agentsFiles: Array<{ path: string; content: string }> };\n\tgetSystemPrompt(): string | undefined;\n\tgetAppendSystemPrompt(): string[];\n\textendResources(paths: ResourceExtensionPaths): void;\n\treload(options?: ResourceLoaderReloadOptions): Promise<void>;\n}\n\nfunction resolvePromptInput(input: string | undefined, description: string): string | undefined {\n\tif (!input) {\n\t\treturn undefined;\n\t}\n\n\tif (existsSync(input)) {\n\t\ttry {\n\t\t\treturn readFileSync(input, \"utf-8\");\n\t\t} catch (error) {\n\t\t\tconsole.error(chalk.yellow(`Warning: Could not read ${description} file ${input}: ${error}`));\n\t\t\treturn input;\n\t\t}\n\t}\n\n\treturn input;\n}\n\nfunction loadContextFileFromDir(dir: string): { path: string; content: string } | null {\n\tconst candidates = [\"AGENTS.md\", \"AGENTS.MD\", \"CLAUDE.md\", \"CLAUDE.MD\"];\n\tfor (const filename of candidates) {\n\t\tconst filePath = join(dir, filename);\n\t\tif (existsSync(filePath)) {\n\t\t\ttry {\n\t\t\t\treturn {\n\t\t\t\t\tpath: filePath,\n\t\t\t\t\tcontent: readFileSync(filePath, \"utf-8\"),\n\t\t\t\t};\n\t\t\t} catch (error) {\n\t\t\t\tconsole.error(chalk.yellow(`Warning: Could not read ${filePath}: ${error}`));\n\t\t\t}\n\t\t}\n\t}\n\treturn null;\n}\n\nexport function loadProjectContextFiles(options: {\n\tcwd: string;\n\tagentDir: string;\n\tprojectTrusted?: boolean;\n}): Array<{ path: string; content: string }> {\n\tconst resolvedCwd = resolvePath(options.cwd);\n\tconst resolvedAgentDir = resolvePath(options.agentDir);\n\n\tconst contextFiles: Array<{ path: string; content: string }> = [];\n\tconst seenPaths = new Set<string>();\n\n\tconst globalContext = loadContextFileFromDir(resolvedAgentDir);\n\tif (globalContext) {\n\t\tcontextFiles.push(globalContext);\n\t\tseenPaths.add(globalContext.path);\n\t}\n\n\tif (options.projectTrusted !== false) {\n\t\tconst ancestorContextFiles: Array<{ path: string; content: string }> = [];\n\n\t\tlet currentDir = resolvedCwd;\n\t\tconst root = resolve(\"/\");\n\n\t\twhile (true) {\n\t\t\tconst contextFile = loadContextFileFromDir(currentDir);\n\t\t\tif (contextFile && !seenPaths.has(contextFile.path)) {\n\t\t\t\tancestorContextFiles.unshift(contextFile);\n\t\t\t\tseenPaths.add(contextFile.path);\n\t\t\t}\n\n\t\t\tif (currentDir === root) break;\n\n\t\t\tconst parentDir = resolve(currentDir, \"..\");\n\t\t\tif (parentDir === currentDir) break;\n\t\t\tcurrentDir = parentDir;\n\t\t}\n\n\t\tcontextFiles.push(...ancestorContextFiles);\n\t}\n\n\treturn contextFiles;\n}\n\nexport interface DefaultResourceLoaderOptions {\n\tcwd: string;\n\tagentDir: string;\n\tsettingsManager?: SettingsManager;\n\teventBus?: EventBus;\n\tadditionalExtensionPaths?: string[];\n\tadditionalSkillPaths?: string[];\n\tadditionalPromptTemplatePaths?: string[];\n\tadditionalThemePaths?: string[];\n\textensionFactories?: ExtensionFactory[];\n\tnoExtensions?: boolean;\n\tnoSkills?: boolean;\n\tnoPromptTemplates?: boolean;\n\tnoThemes?: boolean;\n\tnoContextFiles?: boolean;\n\tsystemPrompt?: string;\n\tappendSystemPrompt?: string[];\n\textensionsOverride?: (base: LoadExtensionsResult) => LoadExtensionsResult;\n\tskillsOverride?: (base: { skills: Skill[]; diagnostics: ResourceDiagnostic[] }) => {\n\t\tskills: Skill[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t};\n\tpromptsOverride?: (base: { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] }) => {\n\t\tprompts: PromptTemplate[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t};\n\tthemesOverride?: (base: { themes: Theme[]; diagnostics: ResourceDiagnostic[] }) => {\n\t\tthemes: Theme[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t};\n\tagentsFilesOverride?: (base: { agentsFiles: Array<{ path: string; content: string }> }) => {\n\t\tagentsFiles: Array<{ path: string; content: string }>;\n\t};\n\tsystemPromptOverride?: (base: string | undefined) => string | undefined;\n\tappendSystemPromptOverride?: (base: string[]) => string[];\n}\n\nexport class DefaultResourceLoader implements ResourceLoader {\n\tprivate cwd: string;\n\tprivate agentDir: string;\n\tprivate settingsManager: SettingsManager;\n\tprivate eventBus: EventBus;\n\tprivate packageManager: DefaultPackageManager;\n\tprivate additionalExtensionPaths: string[];\n\tprivate additionalSkillPaths: string[];\n\tprivate additionalPromptTemplatePaths: string[];\n\tprivate additionalThemePaths: string[];\n\tprivate extensionFactories: ExtensionFactory[];\n\tprivate noExtensions: boolean;\n\tprivate noSkills: boolean;\n\tprivate noPromptTemplates: boolean;\n\tprivate noThemes: boolean;\n\tprivate noContextFiles: boolean;\n\tprivate systemPromptSource?: string;\n\tprivate appendSystemPromptSource?: string[];\n\tprivate extensionsOverride?: (base: LoadExtensionsResult) => LoadExtensionsResult;\n\tprivate skillsOverride?: (base: { skills: Skill[]; diagnostics: ResourceDiagnostic[] }) => {\n\t\tskills: Skill[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t};\n\tprivate promptsOverride?: (base: { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] }) => {\n\t\tprompts: PromptTemplate[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t};\n\tprivate themesOverride?: (base: { themes: Theme[]; diagnostics: ResourceDiagnostic[] }) => {\n\t\tthemes: Theme[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t};\n\tprivate agentsFilesOverride?: (base: { agentsFiles: Array<{ path: string; content: string }> }) => {\n\t\tagentsFiles: Array<{ path: string; content: string }>;\n\t};\n\tprivate systemPromptOverride?: (base: string | undefined) => string | undefined;\n\tprivate appendSystemPromptOverride?: (base: string[]) => string[];\n\n\tprivate extensionsResult: LoadExtensionsResult;\n\tprivate skills: Skill[];\n\tprivate skillDiagnostics: ResourceDiagnostic[];\n\tprivate prompts: PromptTemplate[];\n\tprivate promptDiagnostics: ResourceDiagnostic[];\n\tprivate themes: Theme[];\n\tprivate themeDiagnostics: ResourceDiagnostic[];\n\tprivate agentsFiles: Array<{ path: string; content: string }>;\n\tprivate systemPrompt?: string;\n\tprivate appendSystemPrompt: string[];\n\tprivate lastSkillPaths: string[];\n\tprivate extensionSkillSourceInfos: Map<string, SourceInfo>;\n\tprivate extensionPromptSourceInfos: Map<string, SourceInfo>;\n\tprivate extensionThemeSourceInfos: Map<string, SourceInfo>;\n\tprivate lastPromptPaths: string[];\n\tprivate lastThemePaths: string[];\n\n\tconstructor(options: DefaultResourceLoaderOptions) {\n\t\tthis.cwd = resolvePath(options.cwd);\n\t\tthis.agentDir = resolvePath(options.agentDir);\n\t\tthis.settingsManager = options.settingsManager ?? SettingsManager.create(this.cwd, this.agentDir);\n\t\tthis.eventBus = options.eventBus ?? createEventBus();\n\t\tthis.packageManager = new DefaultPackageManager({\n\t\t\tcwd: this.cwd,\n\t\t\tagentDir: this.agentDir,\n\t\t\tsettingsManager: this.settingsManager,\n\t\t});\n\t\tthis.additionalExtensionPaths = options.additionalExtensionPaths ?? [];\n\t\tthis.additionalSkillPaths = options.additionalSkillPaths ?? [];\n\t\tthis.additionalPromptTemplatePaths = options.additionalPromptTemplatePaths ?? [];\n\t\tthis.additionalThemePaths = options.additionalThemePaths ?? [];\n\t\tthis.extensionFactories = options.extensionFactories ?? [];\n\t\tthis.noExtensions = options.noExtensions ?? false;\n\t\tthis.noSkills = options.noSkills ?? false;\n\t\tthis.noPromptTemplates = options.noPromptTemplates ?? false;\n\t\tthis.noThemes = options.noThemes ?? false;\n\t\tthis.noContextFiles = options.noContextFiles ?? false;\n\t\tthis.systemPromptSource = options.systemPrompt;\n\t\tthis.appendSystemPromptSource = options.appendSystemPrompt;\n\t\tthis.extensionsOverride = options.extensionsOverride;\n\t\tthis.skillsOverride = options.skillsOverride;\n\t\tthis.promptsOverride = options.promptsOverride;\n\t\tthis.themesOverride = options.themesOverride;\n\t\tthis.agentsFilesOverride = options.agentsFilesOverride;\n\t\tthis.systemPromptOverride = options.systemPromptOverride;\n\t\tthis.appendSystemPromptOverride = options.appendSystemPromptOverride;\n\n\t\tthis.extensionsResult = { extensions: [], errors: [], runtime: createExtensionRuntime() };\n\t\tthis.skills = [];\n\t\tthis.skillDiagnostics = [];\n\t\tthis.prompts = [];\n\t\tthis.promptDiagnostics = [];\n\t\tthis.themes = [];\n\t\tthis.themeDiagnostics = [];\n\t\tthis.agentsFiles = [];\n\t\tthis.appendSystemPrompt = [];\n\t\tthis.lastSkillPaths = [];\n\t\tthis.extensionSkillSourceInfos = new Map();\n\t\tthis.extensionPromptSourceInfos = new Map();\n\t\tthis.extensionThemeSourceInfos = new Map();\n\t\tthis.lastPromptPaths = [];\n\t\tthis.lastThemePaths = [];\n\t}\n\n\tgetExtensions(): LoadExtensionsResult {\n\t\treturn this.extensionsResult;\n\t}\n\n\tgetSkills(): { skills: Skill[]; diagnostics: ResourceDiagnostic[] } {\n\t\treturn { skills: this.skills, diagnostics: this.skillDiagnostics };\n\t}\n\n\tgetPrompts(): { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] } {\n\t\treturn { prompts: this.prompts, diagnostics: this.promptDiagnostics };\n\t}\n\n\tgetThemes(): { themes: Theme[]; diagnostics: ResourceDiagnostic[] } {\n\t\treturn { themes: this.themes, diagnostics: this.themeDiagnostics };\n\t}\n\n\tgetAgentsFiles(): { agentsFiles: Array<{ path: string; content: string }> } {\n\t\treturn { agentsFiles: this.agentsFiles };\n\t}\n\n\tgetSystemPrompt(): string | undefined {\n\t\treturn this.systemPrompt;\n\t}\n\n\tgetAppendSystemPrompt(): string[] {\n\t\treturn this.appendSystemPrompt;\n\t}\n\n\textendResources(paths: ResourceExtensionPaths): void {\n\t\tconst skillPaths = this.normalizeExtensionPaths(paths.skillPaths ?? []);\n\t\tconst promptPaths = this.normalizeExtensionPaths(paths.promptPaths ?? []);\n\t\tconst themePaths = this.normalizeExtensionPaths(paths.themePaths ?? []);\n\n\t\tfor (const entry of skillPaths) {\n\t\t\tthis.extensionSkillSourceInfos.set(entry.path, createSourceInfo(entry.path, entry.metadata));\n\t\t}\n\t\tfor (const entry of promptPaths) {\n\t\t\tthis.extensionPromptSourceInfos.set(entry.path, createSourceInfo(entry.path, entry.metadata));\n\t\t}\n\t\tfor (const entry of themePaths) {\n\t\t\tthis.extensionThemeSourceInfos.set(entry.path, createSourceInfo(entry.path, entry.metadata));\n\t\t}\n\n\t\tif (skillPaths.length > 0) {\n\t\t\tthis.lastSkillPaths = this.mergePaths(\n\t\t\t\tthis.lastSkillPaths,\n\t\t\t\tskillPaths.map((entry) => entry.path),\n\t\t\t);\n\t\t\tthis.updateSkillsFromPaths(this.lastSkillPaths);\n\t\t}\n\n\t\tif (promptPaths.length > 0) {\n\t\t\tthis.lastPromptPaths = this.mergePaths(\n\t\t\t\tthis.lastPromptPaths,\n\t\t\t\tpromptPaths.map((entry) => entry.path),\n\t\t\t);\n\t\t\tthis.updatePromptsFromPaths(this.lastPromptPaths);\n\t\t}\n\n\t\tif (themePaths.length > 0) {\n\t\t\tthis.lastThemePaths = this.mergePaths(\n\t\t\t\tthis.lastThemePaths,\n\t\t\t\tthemePaths.map((entry) => entry.path),\n\t\t\t);\n\t\t\tthis.updateThemesFromPaths(this.lastThemePaths);\n\t\t}\n\t}\n\n\tasync reload(options?: ResourceLoaderReloadOptions): Promise<void> {\n\t\tlet preTrustExtensions: LoadExtensionsResult | undefined;\n\t\tif (options?.resolveProjectTrust) {\n\t\t\t// Force untrusted project settings for the bootstrap pass. This keeps project-local\n\t\t\t// extensions/packages out while still loading user/global and temporary CLI extensions.\n\t\t\tthis.settingsManager.setProjectTrusted(false);\n\t\t\tawait this.settingsManager.reload();\n\t\t\tpreTrustExtensions = await this.loadCurrentExtensionSet({ includeInlineFactories: true });\n\t\t\tconst projectTrusted = await options.resolveProjectTrust({ extensionsResult: preTrustExtensions });\n\t\t\tthis.settingsManager.setProjectTrusted(projectTrusted);\n\t\t}\n\n\t\t// reload() preserves SettingsManager.projectTrusted and reloads settings for that trust state.\n\t\tawait this.settingsManager.reload();\n\t\tconst resolvedPaths = await this.packageManager.resolve();\n\t\tconst cliExtensionPaths = await this.packageManager.resolveExtensionSources(this.additionalExtensionPaths, {\n\t\t\ttemporary: true,\n\t\t});\n\t\tconst metadataByPath = new Map<string, PathMetadata>();\n\n\t\tthis.extensionSkillSourceInfos = new Map();\n\t\tthis.extensionPromptSourceInfos = new Map();\n\t\tthis.extensionThemeSourceInfos = new Map();\n\n\t\t// Helper to extract enabled paths and store metadata\n\t\tconst getEnabledResources = (resources: ResolvedResource[]): ResolvedResource[] => {\n\t\t\tfor (const r of resources) {\n\t\t\t\tif (!metadataByPath.has(r.path)) {\n\t\t\t\t\tmetadataByPath.set(r.path, r.metadata);\n\t\t\t\t}\n\t\t\t}\n\t\t\treturn resources.filter((r) => r.enabled);\n\t\t};\n\n\t\tconst getEnabledPaths = (resources: ResolvedResource[]): string[] =>\n\t\t\tgetEnabledResources(resources).map((r) => r.path);\n\t\tconst enabledExtensions = getEnabledPaths(resolvedPaths.extensions);\n\t\tconst enabledSkillResources = getEnabledResources(resolvedPaths.skills);\n\t\tconst enabledPrompts = getEnabledPaths(resolvedPaths.prompts);\n\t\tconst enabledThemes = getEnabledPaths(resolvedPaths.themes);\n\n\t\tconst enabledSkills = enabledSkillResources.map((resource) => this.mapSkillPath(resource, metadataByPath));\n\n\t\t// Add CLI paths metadata\n\t\tfor (const r of cliExtensionPaths.extensions) {\n\t\t\tif (!metadataByPath.has(r.path)) {\n\t\t\t\tmetadataByPath.set(r.path, { source: \"cli\", scope: \"temporary\", origin: \"top-level\" });\n\t\t\t}\n\t\t}\n\t\tfor (const r of cliExtensionPaths.skills) {\n\t\t\tif (!metadataByPath.has(r.path)) {\n\t\t\t\tmetadataByPath.set(r.path, { source: \"cli\", scope: \"temporary\", origin: \"top-level\" });\n\t\t\t}\n\t\t}\n\n\t\tconst cliEnabledExtensions = getEnabledPaths(cliExtensionPaths.extensions);\n\t\tconst cliEnabledSkills = getEnabledPaths(cliExtensionPaths.skills);\n\t\tconst cliEnabledPrompts = getEnabledPaths(cliExtensionPaths.prompts);\n\t\tconst cliEnabledThemes = getEnabledPaths(cliExtensionPaths.themes);\n\n\t\tconst extensionPaths = this.noExtensions\n\t\t\t? cliEnabledExtensions\n\t\t\t: this.mergePaths(cliEnabledExtensions, enabledExtensions);\n\n\t\tconst extensionsResult = await this.loadFinalExtensionSet(extensionPaths, preTrustExtensions);\n\t\tfor (const p of this.additionalExtensionPaths) {\n\t\t\tif (isLocalPath(p)) {\n\t\t\t\tconst resolved = this.resolveResourcePath(p);\n\t\t\t\tif (!existsSync(resolved)) {\n\t\t\t\t\textensionsResult.errors.push({ path: resolved, error: `Extension path does not exist: ${resolved}` });\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tthis.extensionsResult = this.extensionsOverride ? this.extensionsOverride(extensionsResult) : extensionsResult;\n\t\tthis.applyExtensionSourceInfo(this.extensionsResult.extensions, metadataByPath);\n\n\t\tconst skillPaths = this.noSkills\n\t\t\t? this.mergePaths(cliEnabledSkills, this.additionalSkillPaths)\n\t\t\t: this.mergePaths([...cliEnabledSkills, ...enabledSkills], this.additionalSkillPaths);\n\n\t\tthis.lastSkillPaths = skillPaths;\n\t\tthis.updateSkillsFromPaths(skillPaths, metadataByPath);\n\t\tfor (const p of this.additionalSkillPaths) {\n\t\t\tif (isLocalPath(p)) {\n\t\t\t\tconst resolved = this.resolveResourcePath(p);\n\t\t\t\tif (!existsSync(resolved) && !this.skillDiagnostics.some((d) => d.path === resolved)) {\n\t\t\t\t\tthis.skillDiagnostics.push({ type: \"error\", message: \"Skill path does not exist\", path: resolved });\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tconst promptPaths = this.noPromptTemplates\n\t\t\t? this.mergePaths(cliEnabledPrompts, this.additionalPromptTemplatePaths)\n\t\t\t: this.mergePaths([...cliEnabledPrompts, ...enabledPrompts], this.additionalPromptTemplatePaths);\n\n\t\tthis.lastPromptPaths = promptPaths;\n\t\tthis.updatePromptsFromPaths(promptPaths, metadataByPath);\n\t\tfor (const p of this.additionalPromptTemplatePaths) {\n\t\t\tif (isLocalPath(p)) {\n\t\t\t\tconst resolved = this.resolveResourcePath(p);\n\t\t\t\tif (!existsSync(resolved) && !this.promptDiagnostics.some((d) => d.path === resolved)) {\n\t\t\t\t\tthis.promptDiagnostics.push({\n\t\t\t\t\t\ttype: \"error\",\n\t\t\t\t\t\tmessage: \"Prompt template path does not exist\",\n\t\t\t\t\t\tpath: resolved,\n\t\t\t\t\t});\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tconst themePaths = this.noThemes\n\t\t\t? this.mergePaths(cliEnabledThemes, this.additionalThemePaths)\n\t\t\t: this.mergePaths([...cliEnabledThemes, ...enabledThemes], this.additionalThemePaths);\n\n\t\tthis.lastThemePaths = themePaths;\n\t\tthis.updateThemesFromPaths(themePaths, metadataByPath);\n\t\tfor (const p of this.additionalThemePaths) {\n\t\t\tconst resolved = this.resolveResourcePath(p);\n\t\t\tif (!existsSync(resolved) && !this.themeDiagnostics.some((d) => d.path === resolved)) {\n\t\t\t\tthis.themeDiagnostics.push({ type: \"error\", message: \"Theme path does not exist\", path: resolved });\n\t\t\t}\n\t\t}\n\n\t\tconst agentsFiles = {\n\t\t\tagentsFiles: this.noContextFiles\n\t\t\t\t? []\n\t\t\t\t: loadProjectContextFiles({\n\t\t\t\t\t\tcwd: this.cwd,\n\t\t\t\t\t\tagentDir: this.agentDir,\n\t\t\t\t\t\tprojectTrusted: this.settingsManager.isProjectTrusted(),\n\t\t\t\t\t}),\n\t\t};\n\t\tconst resolvedAgentsFiles = this.agentsFilesOverride ? this.agentsFilesOverride(agentsFiles) : agentsFiles;\n\t\tthis.agentsFiles = resolvedAgentsFiles.agentsFiles;\n\n\t\tconst baseSystemPrompt = resolvePromptInput(\n\t\t\tthis.systemPromptSource ?? this.discoverSystemPromptFile(),\n\t\t\t\"system prompt\",\n\t\t);\n\t\tthis.systemPrompt = this.systemPromptOverride ? this.systemPromptOverride(baseSystemPrompt) : baseSystemPrompt;\n\n\t\tconst appendSources =\n\t\t\tthis.appendSystemPromptSource ??\n\t\t\t(this.discoverAppendSystemPromptFile() ? [this.discoverAppendSystemPromptFile()!] : []);\n\t\tconst baseAppend = appendSources\n\t\t\t.map((s) => resolvePromptInput(s, \"append system prompt\"))\n\t\t\t.filter((s): s is string => s !== undefined);\n\t\tthis.appendSystemPrompt = this.appendSystemPromptOverride\n\t\t\t? this.appendSystemPromptOverride(baseAppend)\n\t\t\t: baseAppend;\n\t}\n\n\tprivate async loadCurrentExtensionSet(options: { includeInlineFactories: boolean }): Promise<LoadExtensionsResult> {\n\t\tconst resolvedPaths = await this.packageManager.resolve();\n\t\tconst cliExtensionPaths = await this.packageManager.resolveExtensionSources(this.additionalExtensionPaths, {\n\t\t\ttemporary: true,\n\t\t});\n\t\tconst enabledExtensions = resolvedPaths.extensions.filter((r) => r.enabled).map((r) => r.path);\n\t\tconst cliEnabledExtensions = cliExtensionPaths.extensions.filter((r) => r.enabled).map((r) => r.path);\n\t\tconst extensionPaths = this.noExtensions\n\t\t\t? cliEnabledExtensions\n\t\t\t: this.mergePaths(cliEnabledExtensions, enabledExtensions);\n\t\tconst extensionsResult = await loadExtensions(extensionPaths, this.cwd, this.eventBus);\n\t\tif (!options.includeInlineFactories) {\n\t\t\treturn extensionsResult;\n\t\t}\n\n\t\tconst inlineExtensions = await this.loadExtensionFactories(extensionsResult.runtime);\n\t\textensionsResult.extensions.push(...inlineExtensions.extensions);\n\t\textensionsResult.errors.push(...inlineExtensions.errors);\n\t\treturn extensionsResult;\n\t}\n\n\tprivate resolveExtensionLoadPath(path: string): string {\n\t\treturn resolvePath(path, this.cwd, { normalizeUnicodeSpaces: true });\n\t}\n\n\tprivate async loadFinalExtensionSet(\n\t\textensionPaths: string[],\n\t\tpreTrustExtensions: LoadExtensionsResult | undefined,\n\t): Promise<LoadExtensionsResult> {\n\t\tif (!preTrustExtensions) {\n\t\t\tconst extensionsResult = await loadExtensions(extensionPaths, this.cwd, this.eventBus);\n\t\t\tconst inlineExtensions = await this.loadExtensionFactories(extensionsResult.runtime);\n\t\t\textensionsResult.extensions.push(...inlineExtensions.extensions);\n\t\t\textensionsResult.errors.push(...inlineExtensions.errors);\n\t\t\tthis.addExtensionConflictDiagnostics(extensionsResult);\n\t\t\treturn extensionsResult;\n\t\t}\n\n\t\tconst preloadedByPath = new Map(\n\t\t\tpreTrustExtensions.extensions\n\t\t\t\t.filter((extension) => !extension.path.startsWith(\"<inline:\"))\n\t\t\t\t.map((extension) => [extension.resolvedPath, extension]),\n\t\t);\n\t\tconst failedPreloadPaths = new Set(\n\t\t\tpreTrustExtensions.errors.map((error) => this.resolveExtensionLoadPath(error.path)),\n\t\t);\n\t\tconst remainingPaths = extensionPaths.filter((path) => {\n\t\t\tconst resolvedPath = this.resolveExtensionLoadPath(path);\n\t\t\treturn !preloadedByPath.has(resolvedPath) && !failedPreloadPaths.has(resolvedPath);\n\t\t});\n\t\tconst remainingExtensions = await loadExtensions(\n\t\t\tremainingPaths,\n\t\t\tthis.cwd,\n\t\t\tthis.eventBus,\n\t\t\tpreTrustExtensions.runtime,\n\t\t);\n\t\tconst loadedByPath = new Map(preloadedByPath);\n\t\tfor (const extension of remainingExtensions.extensions) {\n\t\t\tloadedByPath.set(extension.resolvedPath, extension);\n\t\t}\n\n\t\tconst inlineExtensions = preTrustExtensions.extensions.filter((extension) =>\n\t\t\textension.path.startsWith(\"<inline:\"),\n\t\t);\n\t\tconst orderedExtensions = extensionPaths\n\t\t\t.map((path) => loadedByPath.get(this.resolveExtensionLoadPath(path)))\n\t\t\t.filter((extension): extension is Extension => extension !== undefined);\n\t\torderedExtensions.push(...inlineExtensions);\n\n\t\tconst extensionsResult: LoadExtensionsResult = {\n\t\t\textensions: orderedExtensions,\n\t\t\terrors: [...preTrustExtensions.errors, ...remainingExtensions.errors],\n\t\t\truntime: preTrustExtensions.runtime,\n\t\t};\n\t\tthis.addExtensionConflictDiagnostics(extensionsResult);\n\t\treturn extensionsResult;\n\t}\n\n\tprivate addExtensionConflictDiagnostics(extensionsResult: LoadExtensionsResult): void {\n\t\t// Detect extension conflicts (tools, commands, flags with same names from different extensions)\n\t\t// Keep all extensions loaded. Conflicts are reported as diagnostics, and precedence is handled by load order.\n\t\tconst conflicts = this.detectExtensionConflicts(extensionsResult.extensions);\n\t\tfor (const conflict of conflicts) {\n\t\t\textensionsResult.errors.push({ path: conflict.path, error: conflict.message });\n\t\t}\n\t}\n\n\tprivate mapSkillPath(resource: ResolvedResource, metadataByPath: Map<string, PathMetadata>): string {\n\t\tif (resource.metadata.source !== \"auto\" && resource.metadata.origin !== \"package\") {\n\t\t\treturn resource.path;\n\t\t}\n\t\ttry {\n\t\t\tconst stats = statSync(resource.path);\n\t\t\tif (!stats.isDirectory()) {\n\t\t\t\treturn resource.path;\n\t\t\t}\n\t\t} catch {\n\t\t\treturn resource.path;\n\t\t}\n\t\tconst skillFile = join(resource.path, \"SKILL.md\");\n\t\tif (existsSync(skillFile)) {\n\t\t\tif (!metadataByPath.has(skillFile)) {\n\t\t\t\tmetadataByPath.set(skillFile, resource.metadata);\n\t\t\t}\n\t\t\treturn skillFile;\n\t\t}\n\t\treturn resource.path;\n\t}\n\n\tprivate normalizeExtensionPaths(\n\t\tentries: Array<{ path: string; metadata: PathMetadata }>,\n\t): Array<{ path: string; metadata: PathMetadata }> {\n\t\treturn entries.map((entry) => {\n\t\t\tconst metadata = entry.metadata.baseDir\n\t\t\t\t? { ...entry.metadata, baseDir: this.resolveResourcePath(entry.metadata.baseDir) }\n\t\t\t\t: entry.metadata;\n\t\t\treturn {\n\t\t\t\tpath: this.resolveResourcePath(entry.path),\n\t\t\t\tmetadata,\n\t\t\t};\n\t\t});\n\t}\n\n\tprivate updateSkillsFromPaths(skillPaths: string[], metadataByPath?: Map<string, PathMetadata>): void {\n\t\tlet skillsResult: { skills: Skill[]; diagnostics: ResourceDiagnostic[] };\n\t\tif (this.noSkills && skillPaths.length === 0) {\n\t\t\tskillsResult = { skills: [], diagnostics: [] };\n\t\t} else {\n\t\t\tskillsResult = loadSkills({\n\t\t\t\tcwd: this.cwd,\n\t\t\t\tagentDir: this.agentDir,\n\t\t\t\tskillPaths,\n\t\t\t\tincludeDefaults: false,\n\t\t\t});\n\t\t}\n\t\tconst resolvedSkills = this.skillsOverride ? this.skillsOverride(skillsResult) : skillsResult;\n\t\tthis.skills = resolvedSkills.skills.map((skill) => ({\n\t\t\t...skill,\n\t\t\tsourceInfo:\n\t\t\t\tthis.findSourceInfoForPath(skill.filePath, this.extensionSkillSourceInfos, metadataByPath) ??\n\t\t\t\tskill.sourceInfo ??\n\t\t\t\tthis.getDefaultSourceInfoForPath(skill.filePath),\n\t\t}));\n\t\tthis.skillDiagnostics = resolvedSkills.diagnostics;\n\t}\n\n\tprivate updatePromptsFromPaths(promptPaths: string[], metadataByPath?: Map<string, PathMetadata>): void {\n\t\tlet promptsResult: { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] };\n\t\tif (this.noPromptTemplates && promptPaths.length === 0) {\n\t\t\tpromptsResult = { prompts: [], diagnostics: [] };\n\t\t} else {\n\t\t\tconst allPrompts = loadPromptTemplates({\n\t\t\t\tcwd: this.cwd,\n\t\t\t\tagentDir: this.agentDir,\n\t\t\t\tpromptPaths,\n\t\t\t\tincludeDefaults: false,\n\t\t\t});\n\t\t\tpromptsResult = this.dedupePrompts(allPrompts);\n\t\t}\n\t\tconst resolvedPrompts = this.promptsOverride ? this.promptsOverride(promptsResult) : promptsResult;\n\t\tthis.prompts = resolvedPrompts.prompts.map((prompt) => ({\n\t\t\t...prompt,\n\t\t\tsourceInfo:\n\t\t\t\tthis.findSourceInfoForPath(prompt.filePath, this.extensionPromptSourceInfos, metadataByPath) ??\n\t\t\t\tprompt.sourceInfo ??\n\t\t\t\tthis.getDefaultSourceInfoForPath(prompt.filePath),\n\t\t}));\n\t\tthis.promptDiagnostics = resolvedPrompts.diagnostics;\n\t}\n\n\tprivate updateThemesFromPaths(themePaths: string[], metadataByPath?: Map<string, PathMetadata>): void {\n\t\tlet themesResult: { themes: Theme[]; diagnostics: ResourceDiagnostic[] };\n\t\tif (this.noThemes && themePaths.length === 0) {\n\t\t\tthemesResult = { themes: [], diagnostics: [] };\n\t\t} else {\n\t\t\tconst loaded = this.loadThemes(themePaths, false);\n\t\t\tconst deduped = this.dedupeThemes(loaded.themes);\n\t\t\tthemesResult = { themes: deduped.themes, diagnostics: [...loaded.diagnostics, ...deduped.diagnostics] };\n\t\t}\n\t\tconst resolvedThemes = this.themesOverride ? this.themesOverride(themesResult) : themesResult;\n\t\tthis.themes = resolvedThemes.themes.map((theme) => {\n\t\t\tconst sourcePath = theme.sourcePath;\n\t\t\ttheme.sourceInfo = sourcePath\n\t\t\t\t? (this.findSourceInfoForPath(sourcePath, this.extensionThemeSourceInfos, metadataByPath) ??\n\t\t\t\t\ttheme.sourceInfo ??\n\t\t\t\t\tthis.getDefaultSourceInfoForPath(sourcePath))\n\t\t\t\t: theme.sourceInfo;\n\t\t\treturn theme;\n\t\t});\n\t\tthis.themeDiagnostics = resolvedThemes.diagnostics;\n\t}\n\n\tprivate applyExtensionSourceInfo(extensions: Extension[], metadataByPath: Map<string, PathMetadata>): void {\n\t\tfor (const extension of extensions) {\n\t\t\textension.sourceInfo =\n\t\t\t\tthis.findSourceInfoForPath(extension.path, undefined, metadataByPath) ??\n\t\t\t\tthis.getDefaultSourceInfoForPath(extension.path);\n\t\t\tfor (const command of extension.commands.values()) {\n\t\t\t\tcommand.sourceInfo = extension.sourceInfo;\n\t\t\t}\n\t\t\tfor (const tool of extension.tools.values()) {\n\t\t\t\ttool.sourceInfo = extension.sourceInfo;\n\t\t\t}\n\t\t}\n\t}\n\n\tprivate findSourceInfoForPath(\n\t\tresourcePath: string,\n\t\textraSourceInfos?: Map<string, SourceInfo>,\n\t\tmetadataByPath?: Map<string, PathMetadata>,\n\t): SourceInfo | undefined {\n\t\tif (!resourcePath) {\n\t\t\treturn undefined;\n\t\t}\n\n\t\tif (resourcePath.startsWith(\"<\")) {\n\t\t\treturn this.getDefaultSourceInfoForPath(resourcePath);\n\t\t}\n\n\t\tconst normalizedResourcePath = resolve(resourcePath);\n\t\tif (extraSourceInfos) {\n\t\t\tfor (const [sourcePath, sourceInfo] of extraSourceInfos.entries()) {\n\t\t\t\tconst normalizedSourcePath = resolve(sourcePath);\n\t\t\t\tif (\n\t\t\t\t\tnormalizedResourcePath === normalizedSourcePath ||\n\t\t\t\t\tnormalizedResourcePath.startsWith(`${normalizedSourcePath}${sep}`)\n\t\t\t\t) {\n\t\t\t\t\treturn { ...sourceInfo, path: resourcePath };\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tif (metadataByPath) {\n\t\t\tconst exact = metadataByPath.get(normalizedResourcePath) ?? metadataByPath.get(resourcePath);\n\t\t\tif (exact) {\n\t\t\t\treturn createSourceInfo(resourcePath, exact);\n\t\t\t}\n\n\t\t\tfor (const [sourcePath, metadata] of metadataByPath.entries()) {\n\t\t\t\tconst normalizedSourcePath = resolve(sourcePath);\n\t\t\t\tif (\n\t\t\t\t\tnormalizedResourcePath === normalizedSourcePath ||\n\t\t\t\t\tnormalizedResourcePath.startsWith(`${normalizedSourcePath}${sep}`)\n\t\t\t\t) {\n\t\t\t\t\treturn createSourceInfo(resourcePath, metadata);\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\treturn undefined;\n\t}\n\n\tprivate getDefaultSourceInfoForPath(filePath: string): SourceInfo {\n\t\tif (filePath.startsWith(\"<\") && filePath.endsWith(\">\")) {\n\t\t\treturn {\n\t\t\t\tpath: filePath,\n\t\t\t\tsource: filePath.slice(1, -1).split(\":\")[0] || \"temporary\",\n\t\t\t\tscope: \"temporary\",\n\t\t\t\torigin: \"top-level\",\n\t\t\t};\n\t\t}\n\n\t\tconst normalizedPath = resolve(filePath);\n\t\tconst agentRoots = [\n\t\t\tjoin(this.agentDir, \"skills\"),\n\t\t\tjoin(this.agentDir, \"prompts\"),\n\t\t\tjoin(this.agentDir, \"themes\"),\n\t\t\tjoin(this.agentDir, \"extensions\"),\n\t\t];\n\t\tconst projectRoots = [\n\t\t\tjoin(this.cwd, CONFIG_DIR_NAME, \"skills\"),\n\t\t\tjoin(this.cwd, CONFIG_DIR_NAME, \"prompts\"),\n\t\t\tjoin(this.cwd, CONFIG_DIR_NAME, \"themes\"),\n\t\t\tjoin(this.cwd, CONFIG_DIR_NAME, \"extensions\"),\n\t\t];\n\n\t\tfor (const root of agentRoots) {\n\t\t\tif (this.isUnderPath(normalizedPath, root)) {\n\t\t\t\treturn { path: filePath, source: \"local\", scope: \"user\", origin: \"top-level\", baseDir: root };\n\t\t\t}\n\t\t}\n\n\t\tfor (const root of projectRoots) {\n\t\t\tif (this.isUnderPath(normalizedPath, root)) {\n\t\t\t\treturn { path: filePath, source: \"local\", scope: \"project\", origin: \"top-level\", baseDir: root };\n\t\t\t}\n\t\t}\n\n\t\treturn {\n\t\t\tpath: filePath,\n\t\t\tsource: \"local\",\n\t\t\tscope: \"temporary\",\n\t\t\torigin: \"top-level\",\n\t\t\tbaseDir: statSync(normalizedPath).isDirectory() ? normalizedPath : resolve(normalizedPath, \"..\"),\n\t\t};\n\t}\n\n\tprivate mergePaths(primary: string[], additional: string[]): string[] {\n\t\tconst merged: string[] = [];\n\t\tconst seen = new Set<string>();\n\n\t\tfor (const p of [...primary, ...additional]) {\n\t\t\tconst resolved = this.resolveResourcePath(p);\n\t\t\tconst canonicalPath = canonicalizePath(resolved);\n\t\t\tif (seen.has(canonicalPath)) continue;\n\t\t\tseen.add(canonicalPath);\n\t\t\tmerged.push(resolved);\n\t\t}\n\n\t\treturn merged;\n\t}\n\n\tprivate resolveResourcePath(p: string): string {\n\t\treturn resolvePath(p, this.cwd, { trim: true });\n\t}\n\n\tprivate loadThemes(\n\t\tpaths: string[],\n\t\tincludeDefaults: boolean = true,\n\t): {\n\t\tthemes: Theme[];\n\t\tdiagnostics: ResourceDiagnostic[];\n\t} {\n\t\tconst themes: Theme[] = [];\n\t\tconst diagnostics: ResourceDiagnostic[] = [];\n\t\tif (includeDefaults) {\n\t\t\tconst defaultDirs = [join(this.agentDir, \"themes\"), join(this.cwd, CONFIG_DIR_NAME, \"themes\")];\n\n\t\t\tfor (const dir of defaultDirs) {\n\t\t\t\tthis.loadThemesFromDir(dir, themes, diagnostics);\n\t\t\t}\n\t\t}\n\n\t\tfor (const p of paths) {\n\t\t\tconst resolved = this.resolveResourcePath(p);\n\t\t\tif (!existsSync(resolved)) {\n\t\t\t\tdiagnostics.push({ type: \"warning\", message: \"theme path does not exist\", path: resolved });\n\t\t\t\tcontinue;\n\t\t\t}\n\n\t\t\ttry {\n\t\t\t\tconst stats = statSync(resolved);\n\t\t\t\tif (stats.isDirectory()) {\n\t\t\t\t\tthis.loadThemesFromDir(resolved, themes, diagnostics);\n\t\t\t\t} else if (stats.isFile() && resolved.endsWith(\".json\")) {\n\t\t\t\t\tthis.loadThemeFromFile(resolved, themes, diagnostics);\n\t\t\t\t} else {\n\t\t\t\t\tdiagnostics.push({ type: \"warning\", message: \"theme path is not a json file\", path: resolved });\n\t\t\t\t}\n\t\t\t} catch (error) {\n\t\t\t\tconst message = error instanceof Error ? error.message : \"failed to read theme path\";\n\t\t\t\tdiagnostics.push({ type: \"warning\", message, path: resolved });\n\t\t\t}\n\t\t}\n\n\t\treturn { themes, diagnostics };\n\t}\n\n\tprivate loadThemesFromDir(dir: string, themes: Theme[], diagnostics: ResourceDiagnostic[]): void {\n\t\tif (!existsSync(dir)) {\n\t\t\treturn;\n\t\t}\n\n\t\ttry {\n\t\t\tconst entries = readdirSync(dir, { withFileTypes: true });\n\t\t\tfor (const entry of entries) {\n\t\t\t\tlet isFile = entry.isFile();\n\t\t\t\tif (entry.isSymbolicLink()) {\n\t\t\t\t\ttry {\n\t\t\t\t\t\tisFile = statSync(join(dir, entry.name)).isFile();\n\t\t\t\t\t} catch {\n\t\t\t\t\t\tcontinue;\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (!isFile) {\n\t\t\t\t\tcontinue;\n\t\t\t\t}\n\t\t\t\tif (!entry.name.endsWith(\".json\")) {\n\t\t\t\t\tcontinue;\n\t\t\t\t}\n\t\t\t\tthis.loadThemeFromFile(join(dir, entry.name), themes, diagnostics);\n\t\t\t}\n\t\t} catch (error) {\n\t\t\tconst message = error instanceof Error ? error.message : \"failed to read theme directory\";\n\t\t\tdiagnostics.push({ type: \"warning\", message, path: dir });\n\t\t}\n\t}\n\n\tprivate loadThemeFromFile(filePath: string, themes: Theme[], diagnostics: ResourceDiagnostic[]): void {\n\t\ttry {\n\t\t\tthemes.push(loadThemeFromPath(filePath));\n\t\t} catch (error) {\n\t\t\tconst message = error instanceof Error ? error.message : \"failed to load theme\";\n\t\t\tdiagnostics.push({ type: \"warning\", message, path: filePath });\n\t\t}\n\t}\n\n\tprivate async loadExtensionFactories(runtime: ExtensionRuntime): Promise<{\n\t\textensions: Extension[];\n\t\terrors: Array<{ path: string; error: string }>;\n\t}> {\n\t\tconst extensions: Extension[] = [];\n\t\tconst errors: Array<{ path: string; error: string }> = [];\n\n\t\tfor (const [index, factory] of this.extensionFactories.entries()) {\n\t\t\tconst extensionPath = `<inline:${index + 1}>`;\n\t\t\ttry {\n\t\t\t\tconst extension = await loadExtensionFromFactory(factory, this.cwd, this.eventBus, runtime, extensionPath);\n\t\t\t\textensions.push(extension);\n\t\t\t} catch (error) {\n\t\t\t\tconst message = error instanceof Error ? error.message : \"failed to load extension\";\n\t\t\t\terrors.push({ path: extensionPath, error: message });\n\t\t\t}\n\t\t}\n\n\t\treturn { extensions, errors };\n\t}\n\n\tprivate dedupePrompts(prompts: PromptTemplate[]): { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] } {\n\t\tconst seen = new Map<string, PromptTemplate>();\n\t\tconst diagnostics: ResourceDiagnostic[] = [];\n\n\t\tfor (const prompt of prompts) {\n\t\t\tconst existing = seen.get(prompt.name);\n\t\t\tif (existing) {\n\t\t\t\tdiagnostics.push({\n\t\t\t\t\ttype: \"collision\",\n\t\t\t\t\tmessage: `name \"/${prompt.name}\" collision`,\n\t\t\t\t\tpath: prompt.filePath,\n\t\t\t\t\tcollision: {\n\t\t\t\t\t\tresourceType: \"prompt\",\n\t\t\t\t\t\tname: prompt.name,\n\t\t\t\t\t\twinnerPath: existing.filePath,\n\t\t\t\t\t\tloserPath: prompt.filePath,\n\t\t\t\t\t},\n\t\t\t\t});\n\t\t\t} else {\n\t\t\t\tseen.set(prompt.name, prompt);\n\t\t\t}\n\t\t}\n\n\t\treturn { prompts: Array.from(seen.values()), diagnostics };\n\t}\n\n\tprivate dedupeThemes(themes: Theme[]): { themes: Theme[]; diagnostics: ResourceDiagnostic[] } {\n\t\tconst seen = new Map<string, Theme>();\n\t\tconst diagnostics: ResourceDiagnostic[] = [];\n\n\t\tfor (const t of themes) {\n\t\t\tconst name = t.name ?? \"unnamed\";\n\t\t\tconst existing = seen.get(name);\n\t\t\tif (existing) {\n\t\t\t\tdiagnostics.push({\n\t\t\t\t\ttype: \"collision\",\n\t\t\t\t\tmessage: `name \"${name}\" collision`,\n\t\t\t\t\tpath: t.sourcePath,\n\t\t\t\t\tcollision: {\n\t\t\t\t\t\tresourceType: \"theme\",\n\t\t\t\t\t\tname,\n\t\t\t\t\t\twinnerPath: existing.sourcePath ?? \"<builtin>\",\n\t\t\t\t\t\tloserPath: t.sourcePath ?? \"<builtin>\",\n\t\t\t\t\t},\n\t\t\t\t});\n\t\t\t} else {\n\t\t\t\tseen.set(name, t);\n\t\t\t}\n\t\t}\n\n\t\treturn { themes: Array.from(seen.values()), diagnostics };\n\t}\n\n\tprivate discoverSystemPromptFile(): string | undefined {\n\t\tconst projectPath = join(this.cwd, CONFIG_DIR_NAME, \"SYSTEM.md\");\n\t\tif (this.settingsManager.isProjectTrusted() && existsSync(projectPath)) {\n\t\t\treturn projectPath;\n\t\t}\n\n\t\tconst globalPath = join(this.agentDir, \"SYSTEM.md\");\n\t\tif (existsSync(globalPath)) {\n\t\t\treturn globalPath;\n\t\t}\n\n\t\treturn undefined;\n\t}\n\n\tprivate discoverAppendSystemPromptFile(): string | undefined {\n\t\tconst projectPath = join(this.cwd, CONFIG_DIR_NAME, \"APPEND_SYSTEM.md\");\n\t\tif (this.settingsManager.isProjectTrusted() && existsSync(projectPath)) {\n\t\t\treturn projectPath;\n\t\t}\n\n\t\tconst globalPath = join(this.agentDir, \"APPEND_SYSTEM.md\");\n\t\tif (existsSync(globalPath)) {\n\t\t\treturn globalPath;\n\t\t}\n\n\t\treturn undefined;\n\t}\n\n\tprivate isUnderPath(target: string, root: string): boolean {\n\t\tconst normalizedRoot = resolve(root);\n\t\tif (target === normalizedRoot) {\n\t\t\treturn true;\n\t\t}\n\t\tconst prefix = normalizedRoot.endsWith(sep) ? normalizedRoot : `${normalizedRoot}${sep}`;\n\t\treturn target.startsWith(prefix);\n\t}\n\n\tprivate detectExtensionConflicts(extensions: Extension[]): Array<{ path: string; message: string }> {\n\t\tconst conflicts: Array<{ path: string; message: string }> = [];\n\n\t\t// Track which extension registered each tool and flag\n\t\tconst toolOwners = new Map<string, string>();\n\t\tconst flagOwners = new Map<string, string>();\n\n\t\tfor (const ext of extensions) {\n\t\t\t// Check tools\n\t\t\tfor (const toolName of ext.tools.keys()) {\n\t\t\t\tconst existingOwner = toolOwners.get(toolName);\n\t\t\t\tif (existingOwner && existingOwner !== ext.path) {\n\t\t\t\t\tconflicts.push({\n\t\t\t\t\t\tpath: ext.path,\n\t\t\t\t\t\tmessage: `Tool \"${toolName}\" conflicts with ${existingOwner}`,\n\t\t\t\t\t});\n\t\t\t\t} else {\n\t\t\t\t\ttoolOwners.set(toolName, ext.path);\n\t\t\t\t}\n\t\t\t}\n\n\t\t\t// Check flags\n\t\t\tfor (const flagName of ext.flags.keys()) {\n\t\t\t\tconst existingOwner = flagOwners.get(flagName);\n\t\t\t\tif (existingOwner && existingOwner !== ext.path) {\n\t\t\t\t\tconflicts.push({\n\t\t\t\t\t\tpath: ext.path,\n\t\t\t\t\t\tmessage: `Flag \"--${flagName}\" conflicts with ${existingOwner}`,\n\t\t\t\t\t});\n\t\t\t\t} else {\n\t\t\t\t\tflagOwners.set(flagName, ext.path);\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\treturn conflicts;\n\t}\n}\n"]}