@kolisachint/hoocode-agent 0.4.40 → 0.4.42

package/CHANGELOG.md

@@ -1,5 +1,49 @@
 # Changelog
 
+## [0.4.42] - 2026-06-05
+
+### Fixed
+
+- MCP tools failed with `MCP server "<name>" is not connected` once the server's
+  connection was torn down (server process exit, host process churn between turns,
+  or a racing teardown). The tool call gave up immediately with no recovery, and
+  the server config was not retained so it could not reconnect. The loader now
+  retains each server's config and a tool call lazily reconnects from it before
+  failing. The client also now sends the spec-required `notifications/initialized`
+  after `initialize`, the handshake (`initialize`/`tools/list`) is bounded by a
+  timeout so a dead server can't hang startup, and spawned MCP servers are killed
+  when the host process exits so they no longer linger as orphans.
+- Quick-finishing subagents were reported as "stalled". A spawned subagent
+  (`--mode json` with a task id) finished its work and wrote a valid
+  `result.json`, but the child process did not exit on its own: lingering open
+  handles in its runtime kept the event loop alive, so it sat idle until the
+  parent lifeguard SIGKILLed it at the 60s heartbeat threshold (`exit_code: null`,
+  `status: "stalled"`). Spawned subagents now force a clean, flushed exit as soon
+  as their work is done, so they terminate in seconds instead of hanging until the
+  reap. As a defense in depth, the pool now treats a child as successfully
+  completed whenever it produced a verified `result.json`, regardless of exit
+  code, so a kill that races a finished child still returns the real answer.
+
+## [0.4.41] - 2026-06-05
+
+### Added
+
+- Slash commands are now discovered from `.agents/commands/` (project
+  ancestor-walk up to the git root, plus user-level `~/.agents/commands/`), so
+  commands written under the cross-vendor `.agents/` tree round-trip. Precedence
+  is first-match-wins: project `.hoocode` > project `.claude` > project
+  `.agents` (cwd-first) > user `.hoocode` > user `.agents` > user `.claude`.
+
+### Fixed
+
+- Background subagents that finished cleanly were sometimes reported as "stalled".
+  A late lifeguard heartbeat-miss could fire SIGKILL just as a healthy child was
+  already exiting; the kill was a no-op, the child still exited 0 and wrote a valid
+  result.json, but the pool honored the stale stall verdict and discarded the real
+  success. The exit handler now only honors a stalled/timeout kill when the child
+  did not actually complete (non-zero exit or no verified result.json), so a
+  genuine completion always wins over a racing stall verdict.
+
 ## [0.4.40] - 2026-06-05
 
 ## [0.4.39] - 2026-06-05

package/dist/core/resource-loader.d.ts.map

@@ -1 +1 @@
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{ existsSync, readdirSync, readFileSync, statSync } from \"node:fs\";\nimport { homedir } from \"node:os\";\nimport { basename, join, resolve, sep } from \"node:path\";\nimport chalk from \"chalk\";\nimport { CONFIG_DIR_NAME } from \"../config.js\";\nimport { loadThemeFromPath, type Theme } from \"../modes/interactive/theme/theme.js\";\nimport type { ResourceDiagnostic } from \"./diagnostics.js\";\n\nexport type { ResourceCollision, ResourceDiagnostic } from \"./diagnostics.js\";\n\nimport { canonicalizePath, isLocalPath } from \"../utils/paths.js\";\nimport { setAgentManifestPaths } from \"./agent-manifest-paths.js\";\nimport { createEventBus, type EventBus } from \"./event-bus.js\";\nimport { createExtensionRuntime, loadExtensionFromFactory, loadExtensions } from \"./extensions/loader.js\";\nimport type { Extension, ExtensionFactory, ExtensionRuntime, LoadExtensionsResult } from \"./extensions/types.js\";\nimport { DefaultPackageManager, type PathMetadata } from 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{\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\n// Context files (AGENTS.md / CLAUDE.md) are injected into the system prompt on\n// every turn, so their size has a recurring cost on every provider. Warn the\n// user past a soft limit (~2k tokens) and truncate at a hard limit (~10k tokens)\n// so a pasted spec can't silently bloat every request forever.\nconst CONTEXT_FILE_WARN_BYTES = 8 * 1024;\nconst CONTEXT_FILE_MAX_BYTES = 40 * 1024;\nfunction loadContextFileFromDir(dir: string): { file: { path: string; content: string } | null; warnings: string[] } {\n\tconst warnings: string[] = [];\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\tlet content = readFileSync(filePath, \"utf-8\");\n\t\t\t\tconst bytes = Buffer.byteLength(content, \"utf-8\");\n\t\t\t\tif (bytes > CONTEXT_FILE_MAX_BYTES) {\n\t\t\t\t\tcontent =\n\t\t\t\t\t\tcontent.slice(0, CONTEXT_FILE_MAX_BYTES) +\n\t\t\t\t\t\t`\\n\\n[truncated: file exceeded ${CONTEXT_FILE_MAX_BYTES} bytes (~10k tokens); keep context files brief — large specs belong in linked files, not in the system prompt]`;\n\t\t\t\t\twarnings.push(`${basename(filePath)} ${bytes} bytes, truncated.`);\n\t\t\t\t} else if (bytes > CONTEXT_FILE_WARN_BYTES) {\n\t\t\t\t\twarnings.push(\n\t\t\t\t\t\t`${basename(filePath)} ~${Math.round(bytes / 4)} tokens, injected every turn — consider trimming.`,\n\t\t\t\t\t);\n\t\t\t\t}\n\t\t\t\treturn { file: { path: filePath, content }, warnings };\n\t\t\t} catch (error) {\n\t\t\t\twarnings.push(`Could not read ${filePath}: ${error}`);\n\t\t\t}\n\t\t}\n\t}\n\treturn { file: null, warnings };\n}\n\nexport function loadProjectContextFiles(options: { cwd: string; agentDir: string }): {\n\tagentsFiles: Array<{ path: string; content: string }>;\n\twarnings: string[];\n} {\n\tconst resolvedCwd = options.cwd;\n\tconst resolvedAgentDir = options.agentDir;\n\n\tconst contextFiles: Array<{ path: string; content: string }> = [];\n\tconst warnings: string[] = [];\n\tconst seenPaths = new Set<string>();\n\n\tconst globalResult = loadContextFileFromDir(resolvedAgentDir);\n\tif (globalResult.file) {\n\t\tcontextFiles.push(globalResult.file);\n\t\tseenPaths.add(globalResult.file.path);\n\t}\n\twarnings.push(...globalResult.warnings);\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 result = loadContextFileFromDir(currentDir);\n\t\tif (result.file && !seenPaths.has(result.file.path)) {\n\t\t\tancestorContextFiles.unshift(result.file);\n\t\t\tseenPaths.add(result.file.path);\n\t\t}\n\t\twarnings.push(...result.warnings);\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 { agentsFiles: contextFiles, warnings };\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\tadditionalSlashCommandPaths?: string[];\n\tadditionalThemePaths?: string[];\n\textensionFactories?: ExtensionFactory[];\n\tnoExtensions?: boolean;\n\tnoSkills?: boolean;\n\tnoPromptTemplates?: boolean;\n\tnoSlashCommands?: 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 }>; warnings: string[] }) => {\n\t\tagentsFiles: Array<{ path: string; content: string }>;\n\t\twarnings?: 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 additionalSlashCommandPaths: string[];\n\tprivate additionalThemePaths: string[];\n\tprivate extensionFactories: ExtensionFactory[];\n\tprivate noExtensions: boolean;\n\tprivate noSkills: boolean;\n\tprivate noPromptTemplates: boolean;\n\tprivate noSlashCommands: 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: {\n\t\tagentsFiles: Array<{ path: string; content: string }>;\n\t\twarnings: string[];\n\t}) => {\n\t\tagentsFiles: Array<{ path: string; content: string }>;\n\t\twarnings?: 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 agentsFileWarnings: string[];\n\tprivate systemPrompt?: string;\n\tprivate appendSystemPrompt: string[];\n\tprivate lastSkillPaths: string[];\n\tprivate lastAgentPaths: 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 lastSlashCommandPaths: string[];\n\tprivate lastThemePaths: string[];\n\n\tconstructor(options: DefaultResourceLoaderOptions) {\n\t\tthis.cwd = options.cwd;\n\t\tthis.agentDir = 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.additionalSlashCommandPaths = options.additionalSlashCommandPaths ?? [];\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.noSlashCommands = options.noSlashCommands ?? 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.agentsFileWarnings = [];\n\t\tthis.appendSystemPrompt = [];\n\t\tthis.lastSkillPaths = [];\n\t\tthis.lastAgentPaths = [];\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.lastSlashCommandPaths = [];\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\tgetSkillPaths(): string[] {\n\t\treturn [...this.lastSkillPaths];\n\t}\n\n\tgetAgentPaths(): string[] {\n\t\treturn [...this.lastAgentPaths];\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 }>; warnings: string[] } {\n\t\treturn { agentsFiles: this.agentsFiles, warnings: this.agentsFileWarnings };\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\taddAppendSystemPrompt(text: string): void {\n\t\tthis.appendSystemPrompt.push(text);\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, this.lastSlashCommandPaths);\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\t\tconst enabledAgents = getEnabledPaths(resolvedPaths.agents);\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) && !existsSync(p)) {\n\t\t\t\textensionsResult.errors.push({ path: p, error: `Extension path does not exist: ${p}` });\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) && !existsSync(p) && !this.skillDiagnostics.some((d) => d.path === p)) {\n\t\t\t\tthis.skillDiagnostics.push({ type: \"error\", message: \"Skill path does not exist\", path: p });\n\t\t\t}\n\t\t}\n\n\t\t// Prompt templates and slash commands are a single feature sharing one `/name` namespace.\n\t\t// Either disable flag (--no-prompt-templates / --no-slash-commands) turns the whole feature\n\t\t// off; explicit --prompt-template / --slash-command paths still load.\n\t\tconst featureDisabled = this.noPromptTemplates || this.noSlashCommands;\n\t\tconst promptPaths = featureDisabled\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\t// Auto-discover default command directories, mirroring how prompt templates are discovered.\n\t\t// Includes Claude Code slash commands via D7 native import (`.claude/commands/`), at lower\n\t\t// precedence than `.hoocode/commands/`; project wins over user (dedupe is first-match-wins).\n\t\t// Either --no-slash-commands or --no-prompt-templates disables defaults and settings paths;\n\t\t// explicit --slash-command paths still load.\n\t\tconst defaultSlashCommandDirs = [\n\t\t\tjoin(this.cwd, CONFIG_DIR_NAME, \"commands\"),\n\t\t\tjoin(this.cwd, \".claude\", \"commands\"),\n\t\t\tjoin(this.agentDir, \"commands\"),\n\t\t\tjoin(homedir(), \".claude\", \"commands\"),\n\t\t].filter((dir) => existsSync(dir));\n\t\tconst slashCommandPaths = featureDisabled\n\t\t\t? this.mergePaths([], this.additionalSlashCommandPaths)\n\t\t\t: this.mergePaths(\n\t\t\t\t\t[...defaultSlashCommandDirs, ...this.settingsManager.getSlashCommandPaths()],\n\t\t\t\t\tthis.additionalSlashCommandPaths,\n\t\t\t\t);\n\t\tthis.lastSlashCommandPaths = slashCommandPaths;\n\t\tthis.updatePromptsFromPaths(promptPaths, slashCommandPaths, metadataByPath);\n\t\tfor (const p of this.additionalPromptTemplatePaths) {\n\t\t\tif (isLocalPath(p) && !existsSync(p) && !this.promptDiagnostics.some((d) => d.path === p)) {\n\t\t\t\tthis.promptDiagnostics.push({ type: \"error\", message: \"Prompt template path does not exist\", path: p });\n\t\t\t}\n\t\t}\n\t\tfor (const p of this.additionalSlashCommandPaths) {\n\t\t\tif (isLocalPath(p) && !existsSync(p) && !this.promptDiagnostics.some((d) => d.path === p)) {\n\t\t\t\tthis.promptDiagnostics.push({ type: \"error\", message: \"Slash command path does not exist\", path: p });\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\tif (!existsSync(p) && !this.themeDiagnostics.some((d) => d.path === p)) {\n\t\t\t\tthis.themeDiagnostics.push({ type: \"error\", message: \"Theme path does not exist\", path: p });\n\t\t\t}\n\t\t}\n\n\t\tthis.lastAgentPaths = enabledAgents;\n\t\tsetAgentManifestPaths(enabledAgents);\n\n\t\tconst contextResult = this.noContextFiles\n\t\t\t? { agentsFiles: [] as Array<{ path: string; content: string }>, warnings: [] }\n\t\t\t: loadProjectContextFiles({ cwd: this.cwd, agentDir: this.agentDir });\n\t\tconst resolvedAgentsFiles = this.agentsFilesOverride ? this.agentsFilesOverride(contextResult) : contextResult;\n\t\tthis.agentsFiles = resolvedAgentsFiles.agentsFiles;\n\t\tthis.agentsFileWarnings = resolvedAgentsFiles.warnings ?? [];\n\n\t\tconst baseSystemPrompt = resolvePromptInput(this.systemPromptSource, \"system prompt\");\n\t\tthis.systemPrompt = this.systemPromptOverride ? this.systemPromptOverride(baseSystemPrompt) : baseSystemPrompt;\n\n\t\tconst baseAppend = (this.appendSystemPromptSource ?? [])\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\tpath: this.resolveResourcePath(entry.path),\n\t\t\tmetadata: entry.metadata,\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(\n\t\tpromptPaths: string[],\n\t\tslashCommandPaths: string[] = [],\n\t\tmetadataByPath?: Map<string, PathMetadata>,\n\t): void {\n\t\tlet promptsResult: { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] };\n\t\tif (\n\t\t\t(this.noPromptTemplates || this.noSlashCommands) &&\n\t\t\tpromptPaths.length === 0 &&\n\t\t\tslashCommandPaths.length === 0\n\t\t) {\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\tslashCommandPaths,\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\tif (extension.displayName) {\n\t\t\t\t// Preserve inline source info for display-named extensions\n\t\t\t\tfor (const command of extension.commands.values()) {\n\t\t\t\t\tcommand.sourceInfo = extension.sourceInfo;\n\t\t\t\t}\n\t\t\t\tfor (const tool of extension.tools.values()) {\n\t\t\t\t\ttool.sourceInfo = extension.sourceInfo;\n\t\t\t\t}\n\t\t\t\tcontinue;\n\t\t\t}\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, \"commands\"),\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, \"commands\"),\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\tconst trimmed = p.trim();\n\t\tlet expanded = trimmed;\n\t\tif (trimmed === \"~\") {\n\t\t\texpanded = homedir();\n\t\t} else if (trimmed.startsWith(\"~/\")) {\n\t\t\texpanded = join(homedir(), trimmed.slice(2));\n\t\t} else if (trimmed.startsWith(\"~\")) {\n\t\t\texpanded = join(homedir(), trimmed.slice(1));\n\t\t}\n\t\treturn resolve(this.cwd, expanded);\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 = resolve(this.cwd, 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 = factory.displayName ?? `<inline:${index + 1}>`;\n\t\t\ttry {\n\t\t\t\tconst extension = await loadExtensionFromFactory(\n\t\t\t\t\tfactory,\n\t\t\t\t\tthis.cwd,\n\t\t\t\t\tthis.eventBus,\n\t\t\t\t\truntime,\n\t\t\t\t\textensionPath,\n\t\t\t\t\tfactory.displayName,\n\t\t\t\t);\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 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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from \"./package-manager.js\";\nimport type { PromptTemplate } from \"./prompt-templates.js\";\nimport { loadPromptTemplates } from \"./prompt-templates.js\";\nimport { SettingsManager } from \"./settings-manager.js\";\nimport type { Skill } from \"./skills.js\";\nimport { loadSkills } from \"./skills.js\";\nimport { createSourceInfo, type SourceInfo } from \"./source-info.js\";\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\t/**\n\t * Returns the resolved skill paths currently in use.\n\t * Used to forward non-default skill paths to subagent child processes.\n\t */\n\tgetSkillPaths(): string[];\n\t/**\n\t * Returns agent file paths discovered from package manifests (`hoocode.agents`).\n\t * These are passed to loadAgentRegistry() via the module-level store so\n\t * package-distributed agents appear alongside conventionally discovered ones.\n\t */\n\tgetAgentPaths(): string[];\n\tgetPrompts(): { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] };\n\tgetThemes(): { themes: Theme[]; diagnostics: ResourceDiagnostic[] };\n\tgetAgentsFiles(): { agentsFiles: Array<{ path: string; content: string }>; warnings: string[] };\n\tgetSystemPrompt(): string | undefined;\n\tgetAppendSystemPrompt(): string[];\n\taddAppendSystemPrompt(text: string): void;\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\n// Context files (AGENTS.md / CLAUDE.md) are injected into the system prompt on\n// every turn, so their size has a recurring cost on every provider. Warn the\n// user past a soft limit (~2k tokens) and truncate at a hard limit (~10k tokens)\n// so a pasted spec can't silently bloat every request forever.\nconst CONTEXT_FILE_WARN_BYTES = 8 * 1024;\nconst CONTEXT_FILE_MAX_BYTES = 40 * 1024;\nfunction loadContextFileFromDir(dir: string): { file: { path: string; content: string } | null; warnings: string[] } {\n\tconst warnings: string[] = [];\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\tlet content = readFileSync(filePath, \"utf-8\");\n\t\t\t\tconst bytes = Buffer.byteLength(content, \"utf-8\");\n\t\t\t\tif (bytes > CONTEXT_FILE_MAX_BYTES) {\n\t\t\t\t\tcontent =\n\t\t\t\t\t\tcontent.slice(0, CONTEXT_FILE_MAX_BYTES) +\n\t\t\t\t\t\t`\\n\\n[truncated: file exceeded ${CONTEXT_FILE_MAX_BYTES} bytes (~10k tokens); keep context files brief — large specs belong in linked files, not in the system prompt]`;\n\t\t\t\t\twarnings.push(`${basename(filePath)} ${bytes} bytes, truncated.`);\n\t\t\t\t} else if (bytes > CONTEXT_FILE_WARN_BYTES) {\n\t\t\t\t\twarnings.push(\n\t\t\t\t\t\t`${basename(filePath)} ~${Math.round(bytes / 4)} tokens, injected every turn — consider trimming.`,\n\t\t\t\t\t);\n\t\t\t\t}\n\t\t\t\treturn { file: { path: filePath, content }, warnings };\n\t\t\t} catch (error) {\n\t\t\t\twarnings.push(`Could not read ${filePath}: ${error}`);\n\t\t\t}\n\t\t}\n\t}\n\treturn { file: null, warnings };\n}\n\nexport function loadProjectContextFiles(options: { cwd: string; agentDir: string }): {\n\tagentsFiles: Array<{ path: string; content: string }>;\n\twarnings: string[];\n} {\n\tconst resolvedCwd = options.cwd;\n\tconst resolvedAgentDir = options.agentDir;\n\n\tconst contextFiles: Array<{ path: string; content: string }> = [];\n\tconst warnings: string[] = [];\n\tconst seenPaths = new Set<string>();\n\n\tconst globalResult = loadContextFileFromDir(resolvedAgentDir);\n\tif (globalResult.file) {\n\t\tcontextFiles.push(globalResult.file);\n\t\tseenPaths.add(globalResult.file.path);\n\t}\n\twarnings.push(...globalResult.warnings);\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 result = loadContextFileFromDir(currentDir);\n\t\tif (result.file && !seenPaths.has(result.file.path)) {\n\t\t\tancestorContextFiles.unshift(result.file);\n\t\t\tseenPaths.add(result.file.path);\n\t\t}\n\t\twarnings.push(...result.warnings);\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 { agentsFiles: contextFiles, warnings };\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\tadditionalSlashCommandPaths?: string[];\n\tadditionalThemePaths?: string[];\n\textensionFactories?: ExtensionFactory[];\n\tnoExtensions?: boolean;\n\tnoSkills?: boolean;\n\tnoPromptTemplates?: boolean;\n\tnoSlashCommands?: 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 }>; warnings: string[] }) => {\n\t\tagentsFiles: Array<{ path: string; content: string }>;\n\t\twarnings?: 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 additionalSlashCommandPaths: string[];\n\tprivate additionalThemePaths: string[];\n\tprivate extensionFactories: ExtensionFactory[];\n\tprivate noExtensions: boolean;\n\tprivate noSkills: boolean;\n\tprivate noPromptTemplates: boolean;\n\tprivate noSlashCommands: 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: {\n\t\tagentsFiles: Array<{ path: string; content: string }>;\n\t\twarnings: string[];\n\t}) => {\n\t\tagentsFiles: Array<{ path: string; content: string }>;\n\t\twarnings?: 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 agentsFileWarnings: string[];\n\tprivate systemPrompt?: string;\n\tprivate appendSystemPrompt: string[];\n\tprivate lastSkillPaths: string[];\n\tprivate lastAgentPaths: 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 lastSlashCommandPaths: string[];\n\tprivate lastThemePaths: string[];\n\n\tconstructor(options: DefaultResourceLoaderOptions) {\n\t\tthis.cwd = options.cwd;\n\t\tthis.agentDir = 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.additionalSlashCommandPaths = options.additionalSlashCommandPaths ?? [];\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.noSlashCommands = options.noSlashCommands ?? 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.agentsFileWarnings = [];\n\t\tthis.appendSystemPrompt = [];\n\t\tthis.lastSkillPaths = [];\n\t\tthis.lastAgentPaths = [];\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.lastSlashCommandPaths = [];\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\tgetSkillPaths(): string[] {\n\t\treturn [...this.lastSkillPaths];\n\t}\n\n\tgetAgentPaths(): string[] {\n\t\treturn [...this.lastAgentPaths];\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 }>; warnings: string[] } {\n\t\treturn { agentsFiles: this.agentsFiles, warnings: this.agentsFileWarnings };\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\taddAppendSystemPrompt(text: string): void {\n\t\tthis.appendSystemPrompt.push(text);\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, this.lastSlashCommandPaths);\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\t\tconst enabledAgents = getEnabledPaths(resolvedPaths.agents);\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) && !existsSync(p)) {\n\t\t\t\textensionsResult.errors.push({ path: p, error: `Extension path does not exist: ${p}` });\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) && !existsSync(p) && !this.skillDiagnostics.some((d) => d.path === p)) {\n\t\t\t\tthis.skillDiagnostics.push({ type: \"error\", message: \"Skill path does not exist\", path: p });\n\t\t\t}\n\t\t}\n\n\t\t// Prompt templates and slash commands are a single feature sharing one `/name` namespace.\n\t\t// Either disable flag (--no-prompt-templates / --no-slash-commands) turns the whole feature\n\t\t// off; explicit --prompt-template / --slash-command paths still load.\n\t\tconst featureDisabled = this.noPromptTemplates || this.noSlashCommands;\n\t\tconst promptPaths = featureDisabled\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\t// Auto-discover default command directories, mirroring how prompt templates are discovered.\n\t\t// Includes Claude Code slash commands via D7 native import (`.claude/commands/`) and the\n\t\t// cross-vendor `.agents/commands/` surface (project ancestor-walk + global `~/.agents`), so\n\t\t// commands written under `.agents/` round-trip. Precedence is first-match-wins, highest first:\n\t\t// project `.hoocode` > project `.claude` > project `.agents` (cwd-first) > user `.hoocode` >\n\t\t// user `.agents` > user `.claude`. Either --no-slash-commands or --no-prompt-templates disables\n\t\t// defaults and settings paths; explicit --slash-command paths still load.\n\t\tconst defaultSlashCommandDirs = [\n\t\t\tjoin(this.cwd, CONFIG_DIR_NAME, \"commands\"),\n\t\t\tjoin(this.cwd, \".claude\", \"commands\"),\n\t\t\t...collectAgentsAncestorDirs(this.cwd, \"commands\"),\n\t\t\tjoin(this.agentDir, \"commands\"),\n\t\t\tjoin(homedir(), \".agents\", \"commands\"),\n\t\t\tjoin(homedir(), \".claude\", \"commands\"),\n\t\t].filter((dir) => existsSync(dir));\n\t\tconst slashCommandPaths = featureDisabled\n\t\t\t? this.mergePaths([], this.additionalSlashCommandPaths)\n\t\t\t: this.mergePaths(\n\t\t\t\t\t[...defaultSlashCommandDirs, ...this.settingsManager.getSlashCommandPaths()],\n\t\t\t\t\tthis.additionalSlashCommandPaths,\n\t\t\t\t);\n\t\tthis.lastSlashCommandPaths = slashCommandPaths;\n\t\tthis.updatePromptsFromPaths(promptPaths, slashCommandPaths, metadataByPath);\n\t\tfor (const p of this.additionalPromptTemplatePaths) {\n\t\t\tif (isLocalPath(p) && !existsSync(p) && !this.promptDiagnostics.some((d) => d.path === p)) {\n\t\t\t\tthis.promptDiagnostics.push({ type: \"error\", message: \"Prompt template path does not exist\", path: p });\n\t\t\t}\n\t\t}\n\t\tfor (const p of this.additionalSlashCommandPaths) {\n\t\t\tif (isLocalPath(p) && !existsSync(p) && !this.promptDiagnostics.some((d) => d.path === p)) {\n\t\t\t\tthis.promptDiagnostics.push({ type: \"error\", message: \"Slash command path does not exist\", path: p });\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\tif (!existsSync(p) && !this.themeDiagnostics.some((d) => d.path === p)) {\n\t\t\t\tthis.themeDiagnostics.push({ type: \"error\", message: \"Theme path does not exist\", path: p });\n\t\t\t}\n\t\t}\n\n\t\tthis.lastAgentPaths = enabledAgents;\n\t\tsetAgentManifestPaths(enabledAgents);\n\n\t\tconst contextResult = this.noContextFiles\n\t\t\t? { agentsFiles: [] as Array<{ path: string; content: string }>, warnings: [] }\n\t\t\t: loadProjectContextFiles({ cwd: this.cwd, agentDir: this.agentDir });\n\t\tconst resolvedAgentsFiles = this.agentsFilesOverride ? this.agentsFilesOverride(contextResult) : contextResult;\n\t\tthis.agentsFiles = resolvedAgentsFiles.agentsFiles;\n\t\tthis.agentsFileWarnings = resolvedAgentsFiles.warnings ?? [];\n\n\t\tconst baseSystemPrompt = resolvePromptInput(this.systemPromptSource, \"system prompt\");\n\t\tthis.systemPrompt = this.systemPromptOverride ? this.systemPromptOverride(baseSystemPrompt) : baseSystemPrompt;\n\n\t\tconst baseAppend = (this.appendSystemPromptSource ?? [])\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\tpath: this.resolveResourcePath(entry.path),\n\t\t\tmetadata: entry.metadata,\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(\n\t\tpromptPaths: string[],\n\t\tslashCommandPaths: string[] = [],\n\t\tmetadataByPath?: Map<string, PathMetadata>,\n\t): void {\n\t\tlet promptsResult: { prompts: PromptTemplate[]; diagnostics: ResourceDiagnostic[] };\n\t\tif (\n\t\t\t(this.noPromptTemplates || this.noSlashCommands) &&\n\t\t\tpromptPaths.length === 0 &&\n\t\t\tslashCommandPaths.length === 0\n\t\t) {\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\tslashCommandPaths,\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\tif (extension.displayName) {\n\t\t\t\t// Preserve inline source info for display-named extensions\n\t\t\t\tfor (const command of extension.commands.values()) {\n\t\t\t\t\tcommand.sourceInfo = extension.sourceInfo;\n\t\t\t\t}\n\t\t\t\tfor (const tool of extension.tools.values()) {\n\t\t\t\t\ttool.sourceInfo = extension.sourceInfo;\n\t\t\t\t}\n\t\t\t\tcontinue;\n\t\t\t}\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, \"commands\"),\n\t\t\tjoin(this.agentDir, \"themes\"),\n\t\t\tjoin(this.agentDir, \"extensions\"),\n\t\t\tjoin(homedir(), \".agents\", \"commands\"),\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, \"commands\"),\n\t\t\tjoin(this.cwd, CONFIG_DIR_NAME, \"themes\"),\n\t\t\tjoin(this.cwd, CONFIG_DIR_NAME, \"extensions\"),\n\t\t\tjoin(this.cwd, \".agents\", \"commands\"),\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\tconst trimmed = p.trim();\n\t\tlet expanded = trimmed;\n\t\tif (trimmed === \"~\") {\n\t\t\texpanded = homedir();\n\t\t} else if (trimmed.startsWith(\"~/\")) {\n\t\t\texpanded = join(homedir(), trimmed.slice(2));\n\t\t} else if (trimmed.startsWith(\"~\")) {\n\t\t\texpanded = join(homedir(), trimmed.slice(1));\n\t\t}\n\t\treturn resolve(this.cwd, expanded);\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 = resolve(this.cwd, 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 = factory.displayName ?? `<inline:${index + 1}>`;\n\t\t\ttry {\n\t\t\t\tconst extension = await loadExtensionFromFactory(\n\t\t\t\t\tfactory,\n\t\t\t\t\tthis.cwd,\n\t\t\t\t\tthis.eventBus,\n\t\t\t\t\truntime,\n\t\t\t\t\textensionPath,\n\t\t\t\t\tfactory.displayName,\n\t\t\t\t);\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 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"]}

package/dist/core/resource-loader.js

@@ -4,7 +4,7 @@ import { basename, join, resolve, sep } from "node:path";
 import chalk from "chalk";
 import { CONFIG_DIR_NAME } from "../config.js";
 import { loadThemeFromPath } from "../modes/interactive/theme/theme.js";
-import { canonicalizePath, isLocalPath } from "../utils/paths.js";
+import { canonicalizePath, collectAgentsAncestorDirs, isLocalPath } from "../utils/paths.js";
 import { setAgentManifestPaths } from "./agent-manifest-paths.js";
 import { createEventBus } from "./event-bus.js";
 import { createExtensionRuntime, loadExtensionFromFactory, loadExtensions } from "./extensions/loader.js";
@@ -347,14 +347,18 @@ export class DefaultResourceLoader {
             : this.mergePaths([...cliEnabledPrompts, ...enabledPrompts], this.additionalPromptTemplatePaths);
         this.lastPromptPaths = promptPaths;
         // Auto-discover default command directories, mirroring how prompt templates are discovered.
-        // Includes Claude Code slash commands via D7 native import (`.claude/commands/`), at lower
-        // precedence than `.hoocode/commands/`; project wins over user (dedupe is first-match-wins).
-        // Either --no-slash-commands or --no-prompt-templates disables defaults and settings paths;
-        // explicit --slash-command paths still load.
+        // Includes Claude Code slash commands via D7 native import (`.claude/commands/`) and the
+        // cross-vendor `.agents/commands/` surface (project ancestor-walk + global `~/.agents`), so
+        // commands written under `.agents/` round-trip. Precedence is first-match-wins, highest first:
+        // project `.hoocode` > project `.claude` > project `.agents` (cwd-first) > user `.hoocode` >
+        // user `.agents` > user `.claude`. Either --no-slash-commands or --no-prompt-templates disables
+        // defaults and settings paths; explicit --slash-command paths still load.
         const defaultSlashCommandDirs = [
             join(this.cwd, CONFIG_DIR_NAME, "commands"),
             join(this.cwd, ".claude", "commands"),
+            ...collectAgentsAncestorDirs(this.cwd, "commands"),
             join(this.agentDir, "commands"),
+            join(homedir(), ".agents", "commands"),
             join(homedir(), ".claude", "commands"),
         ].filter((dir) => existsSync(dir));
         const slashCommandPaths = featureDisabled
@@ -546,6 +550,7 @@ export class DefaultResourceLoader {
             join(this.agentDir, "commands"),
             join(this.agentDir, "themes"),
             join(this.agentDir, "extensions"),
+            join(homedir(), ".agents", "commands"),
         ];
         const projectRoots = [
             join(this.cwd, CONFIG_DIR_NAME, "skills"),
@@ -553,6 +558,7 @@ export class DefaultResourceLoader {
             join(this.cwd, CONFIG_DIR_NAME, "commands"),
             join(this.cwd, CONFIG_DIR_NAME, "themes"),
             join(this.cwd, CONFIG_DIR_NAME, "extensions"),
+            join(this.cwd, ".agents", "commands"),
         ];
         for (const root of agentRoots) {
             if (this.isUnderPath(normalizedPath, root)) {