agents-inc 0.152.0 → 0.153.0

package/dist/commands/doctor.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../../src/cli/commands/doctor.ts"],"sourcesContent":["import os from \"os\";\nimport path from \"path\";\nimport { BaseCommand } from \"../base-command\";\nimport { getErrorMessage } from \"../utils/errors\";\nimport { EXIT_CODES } from \"../lib/exit-codes\";\nimport { effectivelyExcludedSkillIds, validateProjectConfig } from \"../lib/configuration\";\nimport { loadSource, detectProject } from \"../lib/operations\";\nimport { matrix } from \"../lib/matrix/matrix-provider\";\nimport { discoverLocalSkills } from \"../lib/skills\";\nimport { getStackSkillIds } from \"../lib/stacks\";\nimport { filterExcludedEntries, listAgentMdFiles } from \"../lib/agents\";\nimport { getVerifiedPluginInstallPaths, parseMarketplacePluginRef } from \"../lib/plugins\";\nimport { isHomeDirectory, installBaseDir, resolveInstallPaths } from \"../lib/installation\";\nimport type { MergedSkillsMatrix, ProjectConfig, SkillConfig } from \"../types\";\nimport { fileExists, directoryExists } from \"../utils/fs\";\nimport {\n  CLAUDE_SRC_DIR,\n  CLI_INVOKE_COMMAND,\n  DEFAULT_BRANDING,\n  EJECT_SOURCE,\n  LOCAL_SKILLS_PATH,\n  STANDARD_FILES,\n  UI_SYMBOLS,\n} from \"../consts\";\nimport { countBy, unique } from \"remeda\";\nimport { setVerbose } from \"../utils/logger\";\n\ntype CheckKind = \"config\" | \"skills\" | \"agents\" | \"orphans\" | \"installed\" | \"plugins\" | \"source\";\n\ntype CheckResult = {\n  kind: CheckKind;\n  status: \"pass\" | \"fail\" | \"warn\" | \"skip\";\n  message: string;\n  details?: string[];\n};\n\ntype ConfigCheckOutput = {\n  result: CheckResult;\n  config: ProjectConfig | null;\n};\n\n/** Project-relative path to the config file, shown in doctor messages. */\nconst CONFIG_TS_REL = `${CLAUDE_SRC_DIR}/${STANDARD_FILES.CONFIG_TS}`;\n\nfunction checkConfigValid(config: ProjectConfig | null): ConfigCheckOutput {\n  if (!config) {\n    return {\n      result: {\n        kind: \"config\",\n        status: \"fail\",\n        message: `${CONFIG_TS_REL} not found`,\n        details: [`Run '${CLI_INVOKE_COMMAND} init' to create a configuration`],\n      },\n      config: null,\n    };\n  }\n\n  const validation = validateProjectConfig(config);\n\n  if (!validation.valid) {\n    return {\n      result: {\n        kind: \"config\",\n        status: \"fail\",\n        message: `${CONFIG_TS_REL} has errors`,\n        details: validation.errors,\n      },\n      config: null,\n    };\n  }\n\n  if (validation.warnings.length > 0) {\n    return {\n      result: {\n        kind: \"config\",\n        status: \"warn\",\n        message: `${CONFIG_TS_REL} has warnings`,\n        details: validation.warnings,\n      },\n      config,\n    };\n  }\n\n  return {\n    result: {\n      kind: \"config\",\n      status: \"pass\",\n      message: `${CONFIG_TS_REL} is valid`,\n    },\n    config,\n  };\n}\n\nasync function checkSkillsResolved(\n  config: ProjectConfig,\n  matrix: MergedSkillsMatrix,\n  projectDir: string,\n): Promise<CheckResult> {\n  // config.ts declares skills both directly and through the stack. A global-only\n  // install has a populated skills array and no stack at all, so keying this check\n  // off the stack alone would report \"No skills configured\" for a real install.\n  const excludedIds = effectivelyExcludedSkillIds(config.skills);\n  const stackIds = config.stack ? getStackSkillIds(config.stack) : [];\n  const uniqueSkills = unique([...stackIds, ...config.skills.map((s) => s.id)]).filter(\n    (id) => !excludedIds.has(id),\n  );\n\n  if (uniqueSkills.length === 0) {\n    return {\n      kind: \"skills\",\n      status: \"pass\",\n      message: \"No skills configured\",\n    };\n  }\n\n  const [localResult, globalResult] = await Promise.all([\n    discoverLocalSkills(projectDir),\n    !isHomeDirectory(projectDir) ? discoverLocalSkills(os.homedir()) : null,\n  ]);\n  const localSkillIds = new Set([\n    ...(localResult?.skills.map((s) => s.id) ?? []),\n    ...(globalResult?.skills.map((s) => s.id) ?? []),\n  ]);\n\n  const missingSkills: string[] = [];\n  for (const skillId of uniqueSkills) {\n    const inMatrix = skillId in matrix.skills;\n    const inLocal = localSkillIds.has(skillId);\n    if (!inMatrix && !inLocal) {\n      missingSkills.push(skillId);\n    }\n  }\n\n  if (missingSkills.length > 0) {\n    return {\n      kind: \"skills\",\n      status: \"fail\",\n      message: `${uniqueSkills.length - missingSkills.length}/${uniqueSkills.length} skills found`,\n      details: missingSkills.map((s) => `- ${s} (not found)`),\n    };\n  }\n\n  return {\n    kind: \"skills\",\n    status: \"pass\",\n    message: `${uniqueSkills.length}/${uniqueSkills.length} skills found`,\n  };\n}\n\nasync function checkAgentsCompiled(\n  config: ProjectConfig,\n  projectDir: string,\n): Promise<CheckResult> {\n  const agents = config.agents ?? [];\n\n  if (agents.length === 0) {\n    return {\n      kind: \"agents\",\n      status: \"pass\",\n      message: \"No agents configured\",\n    };\n  }\n\n  const projectAgentsDir = resolveInstallPaths(projectDir, \"project\").agentsDir;\n  const globalAgentsDir = resolveInstallPaths(projectDir, \"global\").agentsDir;\n  const agentChecks = await Promise.all(\n    agents.map(async (agent) => {\n      // Check scope-appropriate directory for the agent\n      const agentsDir = agent.scope === \"global\" ? globalAgentsDir : projectAgentsDir;\n      const agentPath = path.join(agentsDir, `${agent.name}.md`);\n      return { name: agent.name, compiled: await fileExists(agentPath) };\n    }),\n  );\n  const missingAgents = agentChecks.filter((c) => !c.compiled).map((c) => c.name);\n\n  if (missingAgents.length > 0) {\n    return {\n      kind: \"agents\",\n      status: \"warn\",\n      message: `${missingAgents.length} agent${missingAgents.length === 1 ? \"\" : \"s\"} need${missingAgents.length === 1 ? \"s\" : \"\"} recompilation`,\n      details: missingAgents.map((a) => `- ${a} (missing)`),\n    };\n  }\n\n  return {\n    kind: \"agents\",\n    status: \"pass\",\n    message: `${agents.length}/${agents.length} agents compiled`,\n  };\n}\n\nasync function checkNoOrphans(config: ProjectConfig, projectDir: string): Promise<CheckResult> {\n  const projectAgentsDir = resolveInstallPaths(projectDir, \"project\").agentsDir;\n  const globalAgentsDir = resolveInstallPaths(projectDir, \"global\").agentsDir;\n\n  // At home scope both scopes resolve to the same agents directory, so it is\n  // listed once and its files are matched against both scopes' known names.\n  const scopesShareAgentsDir = isHomeDirectory(projectDir);\n\n  const [projectExists, globalExists] = await Promise.all([\n    directoryExists(projectAgentsDir),\n    !scopesShareAgentsDir ? directoryExists(globalAgentsDir) : false,\n  ]);\n\n  if (!projectExists && !globalExists) {\n    return {\n      kind: \"orphans\",\n      status: \"pass\",\n      message: \"No agents directory\",\n    };\n  }\n\n  const projectMdFiles = projectExists ? await listAgentMdFiles(projectAgentsDir) : [];\n  const globalMdFiles = globalExists ? await listAgentMdFiles(globalAgentsDir) : [];\n\n  // Project files: only active project-scoped agents should have .md files here\n  const activeProjectAgents: Set<string> = new Set(\n    (config.agents ?? []).filter((a) => a.scope === \"project\" && !a.excluded).map((a) => a.name),\n  );\n  // Global files: all global-scoped agents (including excluded) still serve other projects\n  const knownGlobalAgents: Set<string> = new Set(\n    (config.agents ?? []).filter((a) => a.scope === \"global\").map((a) => a.name),\n  );\n\n  const knownProjectDirAgents = scopesShareAgentsDir\n    ? new Set([...activeProjectAgents, ...knownGlobalAgents])\n    : activeProjectAgents;\n\n  const orphanedFiles: string[] = [];\n  for (const file of projectMdFiles) {\n    const agentName = file.replace(/\\.md$/, \"\");\n    if (!knownProjectDirAgents.has(agentName)) {\n      orphanedFiles.push(agentName);\n    }\n  }\n  for (const file of globalMdFiles) {\n    const agentName = file.replace(/\\.md$/, \"\");\n    if (!knownGlobalAgents.has(agentName)) {\n      orphanedFiles.push(agentName);\n    }\n  }\n\n  if (orphanedFiles.length > 0) {\n    return {\n      kind: \"orphans\",\n      status: \"warn\",\n      message: `${orphanedFiles.length} orphaned agent file${orphanedFiles.length === 1 ? \"\" : \"s\"}`,\n      details: orphanedFiles.map((f) => `- ${f}.md (not in config)`),\n    };\n  }\n\n  return {\n    kind: \"orphans\",\n    status: \"pass\",\n    message: \"No orphaned agent files\",\n  };\n}\n\nasync function checkSkillsInstalled(\n  config: ProjectConfig,\n  projectDir: string,\n): Promise<CheckResult> {\n  const skills: SkillConfig[] = config.skills ?? [];\n  const ejectSkills = skills.filter((s) => s.source === EJECT_SOURCE);\n\n  if (ejectSkills.length === 0) {\n    return {\n      kind: \"installed\",\n      status: \"pass\",\n      message: \"No eject-mode skills configured\",\n    };\n  }\n\n  const skillChecks = await Promise.all(\n    ejectSkills.map(async (skill) => {\n      const baseDir = installBaseDir(projectDir, skill.scope);\n      const skillMdPath = path.join(baseDir, LOCAL_SKILLS_PATH, skill.id, STANDARD_FILES.SKILL_MD);\n      return { id: skill.id, installed: await fileExists(skillMdPath) };\n    }),\n  );\n  const missingSkills = skillChecks.filter((c) => !c.installed).map((c) => c.id);\n\n  if (missingSkills.length > 0) {\n    return {\n      kind: \"installed\",\n      status: \"warn\",\n      message: `${missingSkills.length} skill${missingSkills.length === 1 ? \"\" : \"s\"} missing from disk`,\n      details: missingSkills.map((s) => `- ${s} (not found in ${LOCAL_SKILLS_PATH}/)`),\n    };\n  }\n\n  return {\n    kind: \"installed\",\n    status: \"pass\",\n    message: `${ejectSkills.length}/${ejectSkills.length} eject-mode skills installed`,\n  };\n}\n\n/**\n * Plugin-mode skills have no files under `.claude/skills/` — they live in the\n * Claude plugin registry. Verifying them means asking the registry for the scope\n * each skill was installed at, not looking on disk.\n */\nasync function checkPluginSkillsInstalled(\n  config: ProjectConfig,\n  projectDir: string,\n): Promise<CheckResult> {\n  const pluginSkills: SkillConfig[] = config.skills.filter((s) => s.source !== EJECT_SOURCE);\n\n  if (pluginSkills.length === 0) {\n    return {\n      kind: \"plugins\",\n      status: \"pass\",\n      message: \"No plugin-mode skills configured\",\n    };\n  }\n\n  const baseDirs = unique(pluginSkills.map((s) => installBaseDir(projectDir, s.scope)));\n  const missingPerBaseDir = await Promise.all(\n    baseDirs.map(async (baseDir) => {\n      const installedIds = new Set(\n        (await getVerifiedPluginInstallPaths(baseDir)).map((plugin) =>\n          parseMarketplacePluginRef(plugin.pluginKey),\n        ),\n      );\n      return pluginSkills\n        .filter((skill) => installBaseDir(projectDir, skill.scope) === baseDir)\n        .filter((skill) => !installedIds.has(skill.id))\n        .map((skill) => skill.id);\n    }),\n  );\n  const missingSkills = missingPerBaseDir.flat();\n\n  if (missingSkills.length > 0) {\n    return {\n      kind: \"plugins\",\n      status: \"warn\",\n      message: `${missingSkills.length} skill${missingSkills.length === 1 ? \"\" : \"s\"} not installed as plugins`,\n      details: missingSkills.map((s) => `- ${s} (no enabled plugin found)`),\n    };\n  }\n\n  return {\n    kind: \"plugins\",\n    status: \"pass\",\n    message: `${pluginSkills.length}/${pluginSkills.length} plugin-mode skills installed`,\n  };\n}\n\nasync function checkSourceReachable(projectDir: string): Promise<CheckResult> {\n  try {\n    const { sourceResult: result } = await loadSource({\n      projectDir,\n    });\n\n    const skillCount = Object.keys(matrix.skills).length;\n    const sourceLabel = result.isLocal ? \"local\" : \"remote\";\n\n    return {\n      kind: \"source\",\n      status: \"pass\",\n      message: `Connected to ${sourceLabel}: ${result.sourcePath}`,\n      details: [`${skillCount} skills available`],\n    };\n  } catch (error) {\n    const message = getErrorMessage(error);\n    return {\n      kind: \"source\",\n      status: \"fail\",\n      message: \"Failed to load source\",\n      details: [message],\n    };\n  }\n}\n\nconst CHECK_WIDTH = 20;\n\nfunction formatCheckName(name: string): string {\n  return name.padEnd(CHECK_WIDTH);\n}\n\nfunction formatStatus(status: CheckResult[\"status\"]): string {\n  switch (status) {\n    case \"pass\":\n      return UI_SYMBOLS.CHECK;\n    case \"fail\":\n      return UI_SYMBOLS.CROSS;\n    case \"warn\":\n      return \"!\";\n    case \"skip\":\n      return \"-\";\n    default: {\n      const _exhaustive: never = status;\n      return _exhaustive;\n    }\n  }\n}\n\nfunction formatCheckLine(name: string, result: CheckResult): string[] {\n  const headerLine = `  ${formatCheckName(name)}${formatStatus(result.status)}  ${result.message}`;\n  const detailLines = (result.details ?? []).map(\n    (detail) => `  ${\" \".repeat(CHECK_WIDTH)}   ${detail}`,\n  );\n  return [headerLine, ...detailLines];\n}\n\nfunction formatSummary(results: CheckResult[]): string {\n  const counts = countBy(results, (r) => r.status);\n  const plural = (n: number, word: string) => `${n} ${word}${n === 1 ? \"\" : \"s\"}`;\n\n  const parts = [\n    `${counts.pass ?? 0} passed`,\n    plural(counts.warn ?? 0, \"warning\"),\n    plural(counts.fail ?? 0, \"error\"),\n  ];\n\n  return `  Summary: ${parts.join(\", \")}`;\n}\n\nconst TIPS: Array<{ kind: CheckKind; status: CheckResult[\"status\"]; tip: string }> = [\n  {\n    kind: \"agents\",\n    status: \"warn\",\n    tip: `  Tip: Run '${CLI_INVOKE_COMMAND} compile' to generate missing agent files`,\n  },\n  {\n    kind: \"config\",\n    status: \"fail\",\n    tip: `  Tip: Run '${CLI_INVOKE_COMMAND} init' to create or fix configuration`,\n  },\n  {\n    kind: \"skills\",\n    status: \"fail\",\n    tip: \"  Tip: Check skill IDs in config match available skills\",\n  },\n  {\n    kind: \"installed\",\n    status: \"warn\",\n    // No command is named on purpose: 'eject skills --force' re-copies every skill in the\n    // source and always targets project scope, so it cannot repair a global-scoped skill\n    // and it litters a plugin-mode project with local skill directories.\n    tip: \"  Tip: Re-eject the missing skills from the source to restore their files\",\n  },\n];\n\nfunction formatTips(results: CheckResult[]): string[] {\n  return TIPS.filter((t) => results.some((r) => r.kind === t.kind && r.status === t.status)).map(\n    (t) => t.tip,\n  );\n}\n\nfunction skippedResult(kind: CheckKind): CheckResult {\n  return { kind, status: \"skip\", message: \"Skipped (config invalid)\" };\n}\n\n/**\n * Wrap a check so a thrown exception becomes a `fail` result instead of crashing the\n * whole doctor run. Per-check isolation ensures one broken check does not mask others.\n */\nasync function safeCheck(kind: CheckKind, fn: () => Promise<CheckResult>): Promise<CheckResult> {\n  try {\n    return await fn();\n  } catch (error) {\n    return { kind, status: \"fail\", message: \"Check threw\", details: [getErrorMessage(error)] };\n  }\n}\n\nexport default class Doctor extends BaseCommand {\n  static summary = \"Diagnose common configuration issues\";\n\n  static description = `Run diagnostic checks on your ${DEFAULT_BRANDING.NAME} configuration to identify issues with config validity, skill resolution, agent compilation, and source connectivity.`;\n\n  static examples = [\"<%= config.bin %> <%= command.id %>\"];\n\n  // Override parent baseFlags to drop --source (not relevant for diagnostics)\n  static baseFlags = {} as (typeof BaseCommand)[\"baseFlags\"];\n\n  static flags = {};\n\n  async run(): Promise<void> {\n    await this.parse(Doctor);\n    setVerbose(true);\n    const projectDir = process.cwd();\n\n    this.printHeader();\n    const results = await this.runAllChecks(projectDir);\n    this.printResults(results);\n\n    if (results.some((r) => r.status === \"fail\")) {\n      this.exit(EXIT_CODES.ERROR);\n    }\n  }\n\n  private printHeader(): void {\n    this.log(\"\");\n    this.log(`${DEFAULT_BRANDING.NAME} Doctor`);\n    this.log(\"\");\n    this.log(\"  Checking configuration health...\");\n    this.log(\"\");\n  }\n\n  private async runAllChecks(projectDir: string): Promise<CheckResult[]> {\n    const detected = await detectProject(projectDir);\n    const { result: configResult, config } = checkConfigValid(detected?.config ?? null);\n    this.logCheck(\"Config Valid\", configResult);\n\n    // loadSource (called by checkSourceReachable) populates the matrix. Run it\n    // before checkSkillsResolved so skills lookups see a populated matrix; if\n    // source fails, skip skills rather than reporting false \"not found\" errors.\n    const sourceResult = await safeCheck(\"source\", () => checkSourceReachable(projectDir));\n\n    const filteredConfig = config ? filterExcludedEntries(config) : null;\n\n    const skillsResult = !config\n      ? skippedResult(\"skills\")\n      : sourceResult.status === \"fail\"\n        ? {\n            kind: \"skills\" as const,\n            status: \"skip\" as const,\n            message: \"Skipped (source unreachable)\",\n          }\n        : await safeCheck(\"skills\", () => checkSkillsResolved(config, matrix, projectDir));\n    this.logCheck(\"Skills Resolved\", skillsResult);\n\n    const agentsResult = filteredConfig\n      ? await safeCheck(\"agents\", () => checkAgentsCompiled(filteredConfig, projectDir))\n      : skippedResult(\"agents\");\n    this.logCheck(\"Agents Compiled\", agentsResult);\n\n    const orphansResult = config\n      ? await safeCheck(\"orphans\", () => checkNoOrphans(config, projectDir))\n      : skippedResult(\"orphans\");\n    this.logCheck(\"No Orphans\", orphansResult);\n\n    const installedResult = filteredConfig\n      ? await safeCheck(\"installed\", () => checkSkillsInstalled(filteredConfig, projectDir))\n      : skippedResult(\"installed\");\n    this.logCheck(\"Skills Installed\", installedResult);\n\n    const pluginsResult = filteredConfig\n      ? await safeCheck(\"plugins\", () => checkPluginSkillsInstalled(filteredConfig, projectDir))\n      : skippedResult(\"plugins\");\n    this.logCheck(\"Plugins Installed\", pluginsResult);\n\n    this.logCheck(\"Source Reachable\", sourceResult);\n\n    return [\n      configResult,\n      skillsResult,\n      agentsResult,\n      orphansResult,\n      installedResult,\n      pluginsResult,\n      sourceResult,\n    ];\n  }\n\n  private logCheck(name: string, result: CheckResult): void {\n    for (const line of formatCheckLine(name, result)) {\n      this.log(line);\n    }\n  }\n\n  private printResults(results: CheckResult[]): void {\n    this.log(\"\");\n    this.log(formatSummary(results));\n\n    const tips = formatTips(results);\n    if (tips.length > 0) {\n      this.log(\"\");\n      for (const tip of tips) {\n        this.log(tip);\n      }\n    }\n\n    this.log(\"\");\n  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+{"version":3,"sources":["../../src/cli/commands/doctor.ts","../../src/cli/lib/source-validator.ts","../../src/cli/lib/content-validator.ts"],"sourcesContent":["import os from \"os\";\nimport path from \"path\";\nimport { BaseCommand } from \"../base-command\";\nimport { getErrorMessage } from \"../utils/errors\";\nimport { EXIT_CODES } from \"../lib/exit-codes\";\nimport {\n  effectivelyExcludedSkillIds,\n  loadProjectConfigFromDir,\n  validateProjectConfig,\n} from \"../lib/configuration\";\nimport { loadSource, detectProject, type DetectedProject } from \"../lib/operations\";\nimport { matrix } from \"../lib/matrix/matrix-provider\";\nimport { discoverLocalSkills } from \"../lib/skills\";\nimport { getStackSkillIds } from \"../lib/stacks\";\nimport { filterExcludedEntries, listAgentMdFiles } from \"../lib/agents\";\nimport { getVerifiedPluginInstallPaths, parseMarketplacePluginRef } from \"../lib/plugins\";\nimport {\n  declaresNoContent,\n  isHomeDirectory,\n  installBaseDir,\n  resolveInstallPaths,\n} from \"../lib/installation\";\nimport { getProjectConfigPath } from \"../lib/configuration\";\nimport { isSourceRepo } from \"../lib/source-validator\";\nimport {\n  listInstalledArtifacts,\n  validateInstalledAgents,\n  validateInstalledPlugins,\n  validateInstalledSkills,\n  validateProjectConfigFile,\n  validateRegisteredSources,\n  type ContentIssue,\n  type ContentValidation,\n} from \"../lib/content-validator\";\nimport type { MergedSkillsMatrix, ProjectConfig, SkillConfig } from \"../types\";\nimport { fileExists, directoryExists } from \"../utils/fs\";\nimport {\n  CLAUDE_SRC_DIR,\n  CLI_INVOKE_COMMAND,\n  DEFAULT_BRANDING,\n  EJECT_SOURCE,\n  LOCAL_SKILLS_PATH,\n  STANDARD_FILES,\n  UI_SYMBOLS,\n} from \"../consts\";\nimport { countBy, unique } from \"remeda\";\nimport { setVerbose } from \"../utils/logger\";\n\ntype CheckKind =\n  | \"config\"\n  | \"config-empty\"\n  | \"skills\"\n  | \"agents\"\n  | \"orphans\"\n  | \"orphans-unowned\"\n  | \"installed\"\n  | \"plugins\"\n  | \"source\"\n  | \"content-config\"\n  | \"content-sources\"\n  | \"content-plugins\"\n  | \"content-skills\"\n  | \"content-agents\";\n\ntype CheckResult = {\n  kind: CheckKind;\n  status: \"pass\" | \"fail\" | \"warn\" | \"skip\";\n  message: string;\n  details?: string[];\n};\n\ntype ConfigCheckOutput = {\n  result: CheckResult;\n  config: ProjectConfig | null;\n};\n\n/**\n * Which state the config these rows describe is in. `detectInstallation` answers \"is there an\n * installation here\", not \"is there a config here\", and hands back the same `null` for an absent\n * file and for one that loads while declaring neither skills nor agents — two states that need\n * different sentences. The state missing from this union is the one that cannot reach this layer:\n * a config that cannot be READ is the content layer's finding, and it skips the operational layer.\n */\ntype ConfigState =\n  | { kind: \"absent\" }\n  | { kind: \"declares-nothing\"; config: ProjectConfig }\n  | { kind: \"loaded\"; config: ProjectConfig };\n\n/** Project-relative path to the config file, shown in doctor messages. */\nconst CONFIG_TS_REL = `${CLAUDE_SRC_DIR}/${STANDARD_FILES.CONFIG_TS}`;\n\n/**\n * The config in THIS directory, and what state it is in. Only this directory: the global fallback\n * is `detectInstallation`'s to make and it has already made it, so a project with no config of its\n * own is absent here whatever the home directory holds — `init` writes exactly the declares-nothing\n * shape as the blank global pair on every project setup, and it is not this project's config.\n *\n * The load cannot throw: `configDirsInPlay` is the same set the content layer just read, and any\n * failure in it skipped this layer entirely.\n */\nasync function resolveConfigState(\n  detected: DetectedProject | null,\n  projectDir: string,\n): Promise<ConfigState> {\n  if (detected?.config) return { kind: \"loaded\", config: detected.config };\n\n  const loaded = await loadProjectConfigFromDir(projectDir);\n  if (!loaded) return { kind: \"absent\" };\n\n  return declaresNoContent(loaded.config)\n    ? { kind: \"declares-nothing\", config: loaded.config }\n    : { kind: \"loaded\", config: loaded.config };\n}\n\nfunction checkConfigValid(state: ConfigState): ConfigCheckOutput {\n  if (state.kind === \"absent\") {\n    return {\n      result: {\n        kind: \"config\",\n        status: \"fail\",\n        message: `${CONFIG_TS_REL} not found`,\n        details: [`Run '${CLI_INVOKE_COMMAND} init' to create a configuration`],\n      },\n      config: null,\n    };\n  }\n\n  // Not a fault and nothing to repair — the file is valid, it just has nothing in it. The config\n  // is still handed on: the rows below describe an empty install truthfully, where a `null` would\n  // have them all report `Skipped (config invalid)` about a config that is valid.\n  if (state.kind === \"declares-nothing\") {\n    return {\n      result: {\n        kind: \"config-empty\",\n        status: \"warn\",\n        message: `${CONFIG_TS_REL} is valid but declares no skills and no agents`,\n      },\n      config: state.config,\n    };\n  }\n\n  const { config } = state;\n  const validation = validateProjectConfig(config);\n\n  if (!validation.valid) {\n    return {\n      result: {\n        kind: \"config\",\n        status: \"fail\",\n        message: `${CONFIG_TS_REL} has errors`,\n        details: validation.errors,\n      },\n      config: null,\n    };\n  }\n\n  if (validation.warnings.length > 0) {\n    return {\n      result: {\n        kind: \"config\",\n        status: \"warn\",\n        message: `${CONFIG_TS_REL} has warnings`,\n        details: validation.warnings,\n      },\n      config,\n    };\n  }\n\n  return {\n    result: {\n      kind: \"config\",\n      status: \"pass\",\n      message: `${CONFIG_TS_REL} is valid`,\n    },\n    config,\n  };\n}\n\nasync function checkSkillsResolved(\n  config: ProjectConfig,\n  matrix: MergedSkillsMatrix,\n  projectDir: string,\n): Promise<CheckResult> {\n  // config.ts declares skills both directly and through the stack. A global-only\n  // install has a populated skills array and no stack at all, so keying this check\n  // off the stack alone would report \"No skills configured\" for a real install.\n  const excludedIds = effectivelyExcludedSkillIds(config.skills);\n  const stackIds = config.stack ? getStackSkillIds(config.stack) : [];\n  const uniqueSkills = unique([...stackIds, ...config.skills.map((s) => s.id)]).filter(\n    (id) => !excludedIds.has(id),\n  );\n\n  if (uniqueSkills.length === 0) {\n    return {\n      kind: \"skills\",\n      status: \"pass\",\n      message: \"No skills configured\",\n    };\n  }\n\n  const [localResult, globalResult] = await Promise.all([\n    discoverLocalSkills(projectDir),\n    !isHomeDirectory(projectDir) ? discoverLocalSkills(os.homedir()) : null,\n  ]);\n  const localSkillIds = new Set([\n    ...(localResult?.skills.map((s) => s.id) ?? []),\n    ...(globalResult?.skills.map((s) => s.id) ?? []),\n  ]);\n\n  const missingSkills = uniqueSkills.filter(\n    (skillId) => !(skillId in matrix.skills) && !localSkillIds.has(skillId),\n  );\n\n  if (missingSkills.length > 0) {\n    return {\n      kind: \"skills\",\n      status: \"fail\",\n      message: `${uniqueSkills.length - missingSkills.length}/${uniqueSkills.length} skills found`,\n      details: missingSkills.map((s) => `- ${s} (not found)`),\n    };\n  }\n\n  return {\n    kind: \"skills\",\n    status: \"pass\",\n    message: `${uniqueSkills.length}/${uniqueSkills.length} skills found`,\n  };\n}\n\nasync function checkAgentsCompiled(\n  config: ProjectConfig,\n  projectDir: string,\n): Promise<CheckResult> {\n  const agents = config.agents;\n\n  if (agents.length === 0) {\n    return {\n      kind: \"agents\",\n      status: \"pass\",\n      message: \"No agents configured\",\n    };\n  }\n\n  const projectAgentsDir = resolveInstallPaths(projectDir, \"project\").agentsDir;\n  const globalAgentsDir = resolveInstallPaths(projectDir, \"global\").agentsDir;\n  const agentChecks = await Promise.all(\n    agents.map(async (agent) => {\n      // Check scope-appropriate directory for the agent\n      const agentsDir = agent.scope === \"global\" ? globalAgentsDir : projectAgentsDir;\n      const agentPath = path.join(agentsDir, `${agent.name}.md`);\n      return { name: agent.name, compiled: await fileExists(agentPath) };\n    }),\n  );\n  const missingAgents = agentChecks.filter((c) => !c.compiled).map((c) => c.name);\n\n  if (missingAgents.length > 0) {\n    return {\n      kind: \"agents\",\n      status: \"warn\",\n      message: `${missingAgents.length} agent${missingAgents.length === 1 ? \"\" : \"s\"} need${missingAgents.length === 1 ? \"s\" : \"\"} recompilation`,\n      details: missingAgents.map((a) => `- ${a} (missing)`),\n    };\n  }\n\n  return {\n    kind: \"agents\",\n    status: \"pass\",\n    message: `${agents.length}/${agents.length} agents compiled`,\n  };\n}\n\nasync function checkNoOrphans(config: ProjectConfig, projectDir: string): Promise<CheckResult> {\n  const projectAgentsDir = resolveInstallPaths(projectDir, \"project\").agentsDir;\n  const globalAgentsDir = resolveInstallPaths(projectDir, \"global\").agentsDir;\n\n  // At home scope both scopes resolve to the same agents directory, so it is\n  // listed once and its files are matched against both scopes' known names.\n  const scopesShareAgentsDir = isHomeDirectory(projectDir);\n\n  const [projectExists, globalExists] = await Promise.all([\n    directoryExists(projectAgentsDir),\n    !scopesShareAgentsDir ? directoryExists(globalAgentsDir) : false,\n  ]);\n\n  if (!projectExists && !globalExists) {\n    return {\n      kind: \"orphans\",\n      status: \"pass\",\n      message: \"No agents directory\",\n    };\n  }\n\n  const projectMdFiles = projectExists ? await listAgentMdFiles(projectAgentsDir) : [];\n  const globalMdFiles = globalExists ? await listAgentMdFiles(globalAgentsDir) : [];\n\n  // Project files: only active project-scoped agents should have .md files here\n  const activeProjectAgents: Set<string> = new Set(\n    config.agents.filter((a) => a.scope === \"project\" && !a.excluded).map((a) => a.name),\n  );\n  // Global files: all global-scoped agents (including excluded) still serve other projects\n  const knownGlobalAgents: Set<string> = new Set(\n    config.agents.filter((a) => a.scope === \"global\").map((a) => a.name),\n  );\n\n  const knownProjectDirAgents = scopesShareAgentsDir\n    ? new Set([...activeProjectAgents, ...knownGlobalAgents])\n    : activeProjectAgents;\n\n  const orphanedFiles = [\n    ...orphanedAgentNames(projectMdFiles, knownProjectDirAgents),\n    ...orphanedAgentNames(globalMdFiles, knownGlobalAgents),\n  ];\n\n  if (orphanedFiles.length > 0) {\n    return {\n      kind: \"orphans\",\n      status: \"warn\",\n      message: plural(orphanedFiles.length, \"orphaned agent file\"),\n      details: orphanedFiles.map((f) => `- ${f}.md (not in config)`),\n    };\n  }\n\n  return {\n    kind: \"orphans\",\n    status: \"pass\",\n    message: \"No orphaned agent files\",\n  };\n}\n\n/**\n * The agents whose compiled `.md` sits in a directory whose roster does not name them. The\n * roster differs per directory — a project directory knows only its own active agents, the\n * global one knows every global-scoped agent including the excluded — so it is a parameter.\n */\nfunction orphanedAgentNames(mdFiles: string[], knownAgents: ReadonlySet<string>): string[] {\n  return mdFiles\n    .map((fileName) => fileName.replace(/\\.md$/, \"\"))\n    .filter((agentName) => !knownAgents.has(agentName));\n}\n\n/**\n * The same row when there is no configuration at all. Ownership is not unknown here, it is\n * settled: nothing declares any of it, so every installed skill directory and compiled agent\n * file is an orphan and the row names them all. It reuses the content layer's walk — those\n * counts four rows above and these names are the same files.\n *\n * A `fail`, where a stray file beside a config is a warning: that warning is earned by the next\n * `compile` pruning what it names, and nothing prunes these. `compile` and `edit` refuse without\n * a config, and `uninstall` cannot identify compiled agents no config declares.\n *\n * With nothing installed the row keeps the skip it has always printed. An empty directory with\n * no config is the state `init` exists for — there is nothing for a configuration to have owned.\n */\nasync function checkUnownedInstallation(projectDir: string): Promise<CheckResult> {\n  const { skills, agents } = await listInstalledArtifacts(projectDir);\n  if (skills.length === 0 && agents.length === 0) return skippedResult(\"orphans\");\n\n  return {\n    kind: \"orphans-unowned\",\n    status: \"fail\",\n    // The per-line \"(not in config)\" the other verdict repeats is said once here instead:\n    // with no configuration it is true of every line, and there are as many lines as files.\n    message: `${countedArtifacts(skills, agents)} installed here, and no configuration declares them`,\n    details: [...skills, ...agents].map((artifact) => `- ${artifact}`),\n  };\n}\n\n/** \"7 skills and 2 agents\", dropping a half with nothing in it rather than saying \"0 agents\". */\nfunction countedArtifacts(skills: string[], agents: string[]): string {\n  return [\n    ...(skills.length > 0 ? [plural(skills.length, \"skill\")] : []),\n    ...(agents.length > 0 ? [plural(agents.length, \"agent\")] : []),\n  ].join(\" and \");\n}\n\nasync function checkSkillsInstalled(\n  config: ProjectConfig,\n  projectDir: string,\n): Promise<CheckResult> {\n  const skills: SkillConfig[] = config.skills;\n  const ejectSkills = skills.filter((s) => s.source === EJECT_SOURCE);\n\n  if (ejectSkills.length === 0) {\n    return {\n      kind: \"installed\",\n      status: \"pass\",\n      message: \"No eject-mode skills configured\",\n    };\n  }\n\n  const skillChecks = await Promise.all(\n    ejectSkills.map(async (skill) => {\n      const baseDir = installBaseDir(projectDir, skill.scope);\n      const skillMdPath = path.join(baseDir, LOCAL_SKILLS_PATH, skill.id, STANDARD_FILES.SKILL_MD);\n      return { id: skill.id, installed: await fileExists(skillMdPath) };\n    }),\n  );\n  const missingSkills = skillChecks.filter((c) => !c.installed).map((c) => c.id);\n\n  if (missingSkills.length > 0) {\n    return {\n      kind: \"installed\",\n      status: \"warn\",\n      message: `${plural(missingSkills.length, \"skill\")} missing from disk`,\n      details: missingSkills.map((s) => `- ${s} (not found in ${LOCAL_SKILLS_PATH}/)`),\n    };\n  }\n\n  return {\n    kind: \"installed\",\n    status: \"pass\",\n    message: `${ejectSkills.length}/${ejectSkills.length} eject-mode skills installed`,\n  };\n}\n\n/**\n * Plugin-mode skills have no files under `.claude/skills/` — they live in the\n * Claude plugin registry. Verifying them means asking the registry for the scope\n * each skill was installed at, not looking on disk.\n */\nasync function checkPluginSkillsInstalled(\n  config: ProjectConfig,\n  projectDir: string,\n): Promise<CheckResult> {\n  const pluginSkills: SkillConfig[] = config.skills.filter((s) => s.source !== EJECT_SOURCE);\n\n  if (pluginSkills.length === 0) {\n    return {\n      kind: \"plugins\",\n      status: \"pass\",\n      message: \"No plugin-mode skills configured\",\n    };\n  }\n\n  const baseDirs = unique(pluginSkills.map((s) => installBaseDir(projectDir, s.scope)));\n  const missingPerBaseDir = await Promise.all(\n    baseDirs.map(async (baseDir) => {\n      const installedIds = new Set(\n        (await getVerifiedPluginInstallPaths(baseDir)).map((plugin) =>\n          parseMarketplacePluginRef(plugin.pluginKey),\n        ),\n      );\n      return pluginSkills\n        .filter((skill) => installBaseDir(projectDir, skill.scope) === baseDir)\n        .filter((skill) => !installedIds.has(skill.id))\n        .map((skill) => skill.id);\n    }),\n  );\n  const missingSkills = missingPerBaseDir.flat();\n\n  if (missingSkills.length > 0) {\n    return {\n      kind: \"plugins\",\n      status: \"warn\",\n      message: `${plural(missingSkills.length, \"skill\")} not installed as plugins`,\n      details: missingSkills.map((s) => `- ${s} (no enabled plugin found)`),\n    };\n  }\n\n  return {\n    kind: \"plugins\",\n    status: \"pass\",\n    message: `${pluginSkills.length}/${pluginSkills.length} plugin-mode skills installed`,\n  };\n}\n\nasync function checkSourceReachable(projectDir: string): Promise<CheckResult> {\n  try {\n    const { sourceResult: result } = await loadSource({\n      projectDir,\n    });\n\n    const skillCount = Object.keys(matrix.skills).length;\n    const sourceLabel = result.isLocal ? \"local\" : \"remote\";\n\n    return {\n      kind: \"source\",\n      status: \"pass\",\n      message: `Connected to ${sourceLabel}: ${result.sourcePath}`,\n      details: [`${skillCount} skills available`],\n    };\n  } catch (error) {\n    const message = getErrorMessage(error);\n    return {\n      kind: \"source\",\n      status: \"fail\",\n      message: \"Failed to load source\",\n      details: [message],\n    };\n  }\n}\n\ntype ContentCheck = {\n  kind: CheckKind;\n  name: string;\n  noun: string;\n  run: (projectDir: string) => Promise<ContentValidation>;\n};\n\n/** A check plus whether it reads config.ts to know WHAT to validate — see {@link CONFIG_CHECK}. */\ntype GatedContentCheck = ContentCheck & { readsConfig: boolean };\n\n/**\n * The config file every other check is read against, so it is validated before any of them and\n * on its own: a file that exists and cannot be parsed is a finding about that file, and every\n * row underneath would be a cascade of it. It carries no gate of its own — it IS the gate.\n */\nconst CONFIG_CHECK: ContentCheck = {\n  kind: \"content-config\",\n  name: \"Config\",\n  noun: \"config\",\n  run: validateProjectConfigFile,\n};\n\n/**\n * The content layer: schema and file-level validation of what is on disk. It runs\n * before the operational layer because an unresolved skill or an uncompiled agent\n * is usually the downstream cascade of a broken metadata.yaml, not its own finding.\n */\nconst CONTENT_CHECKS: GatedContentCheck[] = [\n  {\n    kind: \"content-sources\",\n    name: \"Sources\",\n    noun: \"source\",\n    // The registered sources are the ones config.ts names.\n    readsConfig: true,\n    run: validateRegisteredSources,\n  },\n  {\n    kind: \"content-plugins\",\n    name: \"Plugins\",\n    noun: \"plugin\",\n    readsConfig: false,\n    run: validateInstalledPlugins,\n  },\n  {\n    kind: \"content-skills\",\n    name: \"Skills\",\n    noun: \"skill\",\n    readsConfig: false,\n    run: validateInstalledSkills,\n  },\n  {\n    kind: \"content-agents\",\n    name: \"Agents\",\n    noun: \"agent\",\n    readsConfig: false,\n    run: validateInstalledAgents,\n  },\n];\n\nfunction contentStatus(errors: number, warnings: number): CheckResult[\"status\"] {\n  if (errors > 0) return \"fail\";\n  if (warnings > 0) return \"warn\";\n  return \"pass\";\n}\n\nfunction contentMessage(noun: string, count: number, errors: number, warnings: number): string {\n  // A pass that walked nothing can still report an issue — an unreadable plugin\n  // registry is a finding about the directory, not about a plugin inside it.\n  if (errors === 0 && warnings === 0) {\n    return count === 0 ? `No ${noun}s to validate` : `${plural(count, noun)} validated`;\n  }\n  return `${plural(count, noun)}: ${plural(errors, \"error\")}, ${plural(warnings, \"warning\")}`;\n}\n\nfunction formatContentIssue(issue: ContentIssue): string {\n  const marker = issue.severity === \"error\" ? \"ERROR\" : \"WARN\";\n  return `- [${marker}] ${issue.file}: ${issue.message}`;\n}\n\nfunction toContentResult(check: ContentCheck, validation: ContentValidation): CheckResult {\n  const errors = validation.issues.filter((issue) => issue.severity === \"error\").length;\n  const warnings = validation.issues.length - errors;\n\n  return {\n    kind: check.kind,\n    status: contentStatus(errors, warnings),\n    message: contentMessage(check.noun, validation.count, errors, warnings),\n    details: [\n      ...validation.notes.map((note) => `- ${note}`),\n      ...validation.issues.map(formatContentIssue),\n    ],\n  };\n}\n\nconst CHECK_WIDTH = 20;\n\n/** Section headings and the rows underneath them are indented one step apart. */\nconst SECTION_INDENT = \"  \";\nconst ROW_INDENT = \"    \";\n\nconst SECTION_CONTENT = \"Content checks\";\nconst SECTION_OPERATIONAL = \"Operational checks\";\nconst SKIP_AFTER_CONTENT_ERRORS = \"Skipped — fix the content errors above first\";\nconst SKIP_NO_INSTALLATION = \"Skipped — no installation here (skills source repository)\";\nconst SKIP_CONFIG_UNREADABLE = \"Skipped — the configuration that names them cannot be read\";\n\nfunction plural(count: number, word: string): string {\n  return `${count} ${word}${count === 1 ? \"\" : \"s\"}`;\n}\n\nfunction formatCheckName(name: string): string {\n  return name.padEnd(CHECK_WIDTH);\n}\n\nfunction formatStatus(status: CheckResult[\"status\"]): string {\n  switch (status) {\n    case \"pass\":\n      return UI_SYMBOLS.CHECK;\n    case \"fail\":\n      return UI_SYMBOLS.CROSS;\n    case \"warn\":\n      return \"!\";\n    case \"skip\":\n      return \"-\";\n    default: {\n      const _exhaustive: never = status;\n      return _exhaustive;\n    }\n  }\n}\n\nfunction formatCheckLine(name: string, result: CheckResult): string[] {\n  const headerLine = `${ROW_INDENT}${formatCheckName(name)}${formatStatus(result.status)}  ${result.message}`;\n  const detailLines = (result.details ?? []).map(\n    (detail) => `${ROW_INDENT}${\" \".repeat(CHECK_WIDTH)}   ${detail}`,\n  );\n  return [headerLine, ...detailLines];\n}\n\nfunction formatSummary(results: CheckResult[]): string {\n  const counts = countBy(results, (r) => r.status);\n\n  const parts = [\n    `${counts.pass ?? 0} passed`,\n    plural(counts.warn ?? 0, \"warning\"),\n    plural(counts.fail ?? 0, \"error\"),\n  ];\n\n  return `${SECTION_INDENT}Summary: ${parts.join(\", \")}`;\n}\n\nconst TIPS: Array<{ kind: CheckKind; status: CheckResult[\"status\"]; tip: string }> = [\n  {\n    kind: \"agents\",\n    status: \"warn\",\n    tip: `  Tip: Run '${CLI_INVOKE_COMMAND} compile' to generate missing agent files`,\n  },\n  {\n    kind: \"config\",\n    status: \"fail\",\n    tip: `  Tip: Run '${CLI_INVOKE_COMMAND} init' to create or fix configuration`,\n  },\n  {\n    // The remedy for a valid config with nothing in it. Not the tip above: there is nothing to\n    // create and nothing to fix. `init` on this config opens the wizard rather than the dashboard\n    // — that is what the detection returning null is FOR — so it is the way to fill it in.\n    kind: \"config-empty\",\n    status: \"warn\",\n    tip: `  Tip: Nothing is configured yet — run '${CLI_INVOKE_COMMAND} init' to choose skills and sub-agents`,\n  },\n  {\n    // The one remedy that applies to a config that cannot be read. `init` does not clear such a\n    // file — it refuses it — so the tip above would send the reader in a circle; this is the same\n    // way out `edit` and `init` themselves name, worded the same way.\n    kind: \"content-config\",\n    status: \"fail\",\n    tip: `  Tip: There is no automatic repair — recreate the configuration: '${CLI_INVOKE_COMMAND} uninstall' still works on a config it cannot read, then '${CLI_INVOKE_COMMAND} init'`,\n  },\n  {\n    // Printed beside the config tip above, which says how to get a configuration back and\n    // nothing about the files that outlived the old one. Both halves are named with what they\n    // actually do: `uninstall` matches skill directories by their own `forked-from` metadata,\n    // so it clears them without a config — and identifies compiled agents only through one.\n    kind: \"orphans-unowned\",\n    status: \"fail\",\n    tip: `  Tip: Nothing declares the files above — '${CLI_INVOKE_COMMAND} init' writes a configuration that can own them again, or '${CLI_INVOKE_COMMAND} uninstall' removes the installed skills (the compiled agents outlive it: identifying them needs the configuration that is gone)`,\n  },\n  {\n    kind: \"skills\",\n    status: \"fail\",\n    tip: \"  Tip: Check skill IDs in config match available skills\",\n  },\n  {\n    kind: \"installed\",\n    status: \"warn\",\n    // No command is named on purpose: 'eject skills --force' re-copies every skill in the\n    // source and always targets project scope, so it cannot repair a global-scoped skill\n    // and it litters a plugin-mode project with local skill directories.\n    tip: \"  Tip: Re-eject the missing skills from the source to restore their files\",\n  },\n];\n\nfunction formatTips(results: CheckResult[]): string[] {\n  return TIPS.filter((t) => results.some((r) => r.kind === t.kind && r.status === t.status)).map(\n    (t) => t.tip,\n  );\n}\n\nfunction skippedResult(kind: CheckKind): CheckResult {\n  return { kind, status: \"skip\", message: \"Skipped (config invalid)\" };\n}\n\n/**\n * The skills row when the source never loaded. Distinct from {@link skippedResult}: the config\n * is fine, and what is missing is the matrix to resolve its skills against.\n */\nfunction sourceUnreachableSkillsResult(): CheckResult {\n  return { kind: \"skills\", status: \"skip\", message: \"Skipped (source unreachable)\" };\n}\n\nfunction skippedContentResult(kind: CheckKind): CheckResult {\n  return { kind, status: \"skip\", message: SKIP_CONFIG_UNREADABLE };\n}\n\nfunction runContentCheck(check: ContentCheck, projectDir: string): Promise<CheckResult> {\n  return safeCheck(check.kind, async () => toContentResult(check, await check.run(projectDir)));\n}\n\n/**\n * Wrap a check so a thrown exception becomes a `fail` result instead of crashing the\n * whole doctor run. Per-check isolation ensures one broken check does not mask others.\n */\nasync function safeCheck(kind: CheckKind, fn: () => Promise<CheckResult>): Promise<CheckResult> {\n  try {\n    return await fn();\n  } catch (error) {\n    return { kind, status: \"fail\", message: \"Check threw\", details: [getErrorMessage(error)] };\n  }\n}\n\nexport default class Doctor extends BaseCommand {\n  static summary = \"Diagnose common configuration issues\";\n\n  static description = `Run diagnostic checks on your ${DEFAULT_BRANDING.NAME} configuration to identify issues with config validity, skill resolution, agent compilation, and source connectivity.`;\n\n  static examples = [\"<%= config.bin %> <%= command.id %>\"];\n\n  static flags = {};\n\n  async run(): Promise<void> {\n    await this.parse(Doctor);\n    setVerbose(true);\n    const projectDir = process.cwd();\n\n    this.printHeader();\n    const contentResults = await this.runContentChecks(projectDir);\n    const operationalResults = await this.runOperationalChecks(projectDir, contentResults);\n    const results = [...contentResults, ...operationalResults];\n\n    this.printResults(results);\n\n    if (results.some((r) => r.status === \"fail\")) {\n      this.exit(EXIT_CODES.ERROR);\n    }\n  }\n\n  private printHeader(): void {\n    this.log(\"\");\n    this.log(`${DEFAULT_BRANDING.NAME} Doctor`);\n    this.log(\"\");\n    this.log(`${SECTION_INDENT}Checking configuration health...`);\n    this.log(\"\");\n  }\n\n  /**\n   * The config is checked first and alone. A check that reads it to know what to validate would\n   * otherwise ask a file already reported as unreadable — and asking is what emitted the loader's\n   * own failure line once per read, spliced between these rows. Everything that walks installed\n   * content on disk still runs: it says something true whatever the config is in.\n   */\n  private async runContentChecks(projectDir: string): Promise<CheckResult[]> {\n    this.log(`${SECTION_INDENT}${SECTION_CONTENT}`);\n\n    const configResult = await runContentCheck(CONFIG_CHECK, projectDir);\n    const configUnreadable = configResult.status === \"fail\";\n\n    const rows = await Promise.all(\n      CONTENT_CHECKS.map(async (check) => ({\n        name: check.name,\n        result:\n          check.readsConfig && configUnreadable\n            ? skippedContentResult(check.kind)\n            : await runContentCheck(check, projectDir),\n      })),\n    );\n\n    const allRows = [{ name: CONFIG_CHECK.name, result: configResult }, ...rows];\n\n    for (const row of allRows) {\n      this.logCheck(row.name, row.result);\n    }\n\n    return allRows.map((row) => row.result);\n  }\n\n  /**\n   * The operational layer runs only when it can say something the reader can act on:\n   * not after content errors (its findings would be their cascades), and not in a\n   * source repository with nothing installed (a marketplace author has no install\n   * for it to describe).\n   */\n  private async runOperationalChecks(\n    projectDir: string,\n    contentResults: CheckResult[],\n  ): Promise<CheckResult[]> {\n    this.log(\"\");\n    this.log(`${SECTION_INDENT}${SECTION_OPERATIONAL}`);\n\n    if (contentResults.some((r) => r.status === \"fail\")) {\n      this.log(`${ROW_INDENT}${SKIP_AFTER_CONTENT_ERRORS}`);\n      return [];\n    }\n\n    const detected = await detectProject(projectDir);\n    if (!detected && (await this.isUninstalledSourceRepo(projectDir))) {\n      this.log(`${ROW_INDENT}${SKIP_NO_INSTALLATION}`);\n      return [];\n    }\n\n    return this.runAllChecks(projectDir, await resolveConfigState(detected, projectDir));\n  }\n\n  /**\n   * A config file that exists but failed to load also detects as \"no project\", and\n   * that is a finding rather than an absence — so the skip requires no config file\n   * at all, not merely no usable one.\n   */\n  private async isUninstalledSourceRepo(projectDir: string): Promise<boolean> {\n    if (await fileExists(getProjectConfigPath(projectDir))) return false;\n    return isSourceRepo(projectDir);\n  }\n\n  private async runAllChecks(projectDir: string, configState: ConfigState): Promise<CheckResult[]> {\n    const { result: configResult, config } = checkConfigValid(configState);\n    this.logCheck(\"Config Valid\", configResult);\n\n    // loadSource (called by checkSourceReachable) populates the matrix. Run it\n    // before checkSkillsResolved so skills lookups see a populated matrix; if\n    // source fails, skip skills rather than reporting false \"not found\" errors.\n    const sourceResult = await safeCheck(\"source\", () => checkSourceReachable(projectDir));\n\n    const filteredConfig = config ? filterExcludedEntries(config) : null;\n\n    const skillsResult = await this.resolveSkillsCheck(config, sourceResult, projectDir);\n    this.logCheck(\"Skills Resolved\", skillsResult);\n\n    const agentsResult = filteredConfig\n      ? await safeCheck(\"agents\", () => checkAgentsCompiled(filteredConfig, projectDir))\n      : skippedResult(\"agents\");\n    this.logCheck(\"Agents Compiled\", agentsResult);\n\n    const orphansResult = await this.resolveOrphansCheck(config, configState, projectDir);\n    this.logCheck(\"No Orphans\", orphansResult);\n\n    const installedResult = filteredConfig\n      ? await safeCheck(\"installed\", () => checkSkillsInstalled(filteredConfig, projectDir))\n      : skippedResult(\"installed\");\n    this.logCheck(\"Skills Installed\", installedResult);\n\n    const pluginsResult = filteredConfig\n      ? await safeCheck(\"plugins\", () => checkPluginSkillsInstalled(filteredConfig, projectDir))\n      : skippedResult(\"plugins\");\n    this.logCheck(\"Plugins Installed\", pluginsResult);\n\n    this.logCheck(\"Source Reachable\", sourceResult);\n\n    return [\n      configResult,\n      skillsResult,\n      agentsResult,\n      orphansResult,\n      installedResult,\n      pluginsResult,\n      sourceResult,\n    ];\n  }\n\n  /**\n   * The orphan row, and which question it can answer. With a config it names the compiled\n   * agents that config does not; with no config at all every installed file is unowned and it\n   * names all of them. It skips for the one state left — a config that loads and fails\n   * validation — because there the file that says who owns what has already been rejected, and\n   * an installation must not be called stranded on the strength of one nobody can trust.\n   */\n  private async resolveOrphansCheck(\n    config: ProjectConfig | null,\n    configState: ConfigState,\n    projectDir: string,\n  ): Promise<CheckResult> {\n    if (config) return safeCheck(\"orphans\", () => checkNoOrphans(config, projectDir));\n    if (configState.kind === \"absent\") {\n      return safeCheck(\"orphans\", () => checkUnownedInstallation(projectDir));\n    }\n    return skippedResult(\"orphans\");\n  }\n\n  /**\n   * The skills row, and the two states in which it cannot be computed: no config to read the\n   * skills out of, and a source that never loaded — so there is no populated matrix to resolve\n   * them against, and every configured skill would be reported \"not found\".\n   */\n  private async resolveSkillsCheck(\n    config: ProjectConfig | null,\n    sourceResult: CheckResult,\n    projectDir: string,\n  ): Promise<CheckResult> {\n    if (!config) return skippedResult(\"skills\");\n    if (sourceResult.status === \"fail\") return sourceUnreachableSkillsResult();\n\n    return safeCheck(\"skills\", () => checkSkillsResolved(config, matrix, projectDir));\n  }\n\n  private logCheck(name: string, result: CheckResult): void {\n    for (const line of formatCheckLine(name, result)) {\n      this.log(line);\n    }\n  }\n\n  private printResults(results: CheckResult[]): void {\n    this.log(\"\");\n    this.log(formatSummary(results));\n\n    const tips = formatTips(results);\n    if (tips.length > 0) {\n      this.log(\"\");\n      for (const tip of tips) {\n        this.log(tip);\n      }\n    }\n\n    this.log(\"\");\n  }\n}\n","import path from \"path\";\nimport { isRecord } from \"../utils/type-guards.js\";\nimport { parse as parseYaml } from \"yaml\";\nimport { z } from \"zod\";\nimport { glob, readFile, fileExists, directoryExists } from \"../utils/fs\";\nimport {\n  DIRS,\n  SKILL_CATEGORIES_PATH,\n  SKILL_RULES_PATH,\n  SKILLS_DIR_PATH,\n  STACKS_FILE_PATH,\n  STANDARD_FILES,\n} from \"../consts\";\nimport {\n  agentYamlGenerationSchema,\n  metadataValidationSchema,\n  splitMetadataValidationIssues,\n  validateSkillMetadata,\n  skillCategoriesFileSchema,\n  skillRulesFileSchema,\n  stackConfigValidationSchema,\n  stacksConfigSchema,\n} from \"./schemas\";\nimport { parseFrontmatter } from \"./loading/loader\";\nimport { loadConfig, loadProjectSourceConfig } from \"./configuration\";\nimport { checkMatrixHealth } from \"./matrix\";\nimport { loadSkillsMatrixFromSource } from \"./loading/source-loader\";\nimport { matrix } from \"./matrix/matrix-provider\";\nimport { getErrorMessage } from \"../utils/errors\";\nimport { formatZodErrors } from \"./schema-validator\";\n\nexport type SourceValidationIssue = {\n  severity: \"error\" | \"warning\";\n  file: string;\n  message: string;\n};\n\nexport type SourceValidationResult = {\n  issues: SourceValidationIssue[];\n  skillCount: number;\n  errorCount: number;\n  warningCount: number;\n};\n\n/**\n * True when `dir` is itself a skills source repository — it carries the skills tree\n * `validateSource` walks, at `src/skills/` or wherever its own source config points.\n * A marketplace author's checkout answers yes; a consumer project answers no.\n */\nexport async function isSourceRepo(dir: string): Promise<boolean> {\n  const sourceConfig = await loadProjectSourceConfig(dir);\n  return directoryExists(path.join(dir, sourceConfig?.skillsDir ?? SKILLS_DIR_PATH));\n}\n\n/** Checks if a key uses snake_case (has underscore between lowercase letters) */\nexport function isSnakeCase(key: string): boolean {\n  return /[a-z]_[a-z]/.test(key);\n}\n\n/**\n * Checks top-level keys for snake_case usage (camelCase is the convention).\n * Non-object input yields no issues.\n */\nexport function checkSnakeCaseKeys(rawMetadata: unknown, relPath: string): SourceValidationIssue[] {\n  if (!isRecord(rawMetadata)) return [];\n\n  return Object.keys(rawMetadata)\n    .filter(isSnakeCase)\n    .map((key) => ({\n      severity: \"error\" as const,\n      file: relPath,\n      message: `Key '${key}' uses snake_case — use camelCase instead`,\n    }));\n}\n\n/**\n * Warns when a skill directory's name does not equal the skill's machine id\n * (SKILL.md frontmatter `name`) — the key the loader registers the skill under.\n * Warning, not error: the loader still loads the skill by its id, but the\n * directory no longer signals which skill it contains.\n */\nexport function checkDirNameMatchesSkillId(\n  skillId: string,\n  relPath: string,\n  dirName: string,\n): SourceValidationIssue[] {\n  if (skillId === dirName) return [];\n  return [\n    {\n      severity: \"warning\",\n      file: relPath,\n      message: `Directory name '${dirName}' does not match skill id '${skillId}'`,\n    },\n  ];\n}\n\n/**\n * Reads a skill directory's SKILL.md frontmatter and checks the directory name\n * against the skill's machine id. When the id cannot be read (unreadable file or\n * missing/invalid frontmatter), reports that the check could not run.\n */\nasync function checkSkillDirName(\n  skillsDir: string,\n  skillsDirRelPath: string,\n  skillDir: string,\n): Promise<SourceValidationIssue[]> {\n  const dirName = path.basename(skillDir);\n  const skillMdRelPath = path.join(skillsDirRelPath, skillDir, STANDARD_FILES.SKILL_MD);\n\n  try {\n    const content = await readFile(path.join(skillsDir, skillDir, STANDARD_FILES.SKILL_MD));\n    const frontmatter = parseFrontmatter(content, skillMdRelPath);\n\n    if (frontmatter === null) {\n      return [\n        {\n          severity: \"warning\",\n          file: skillMdRelPath,\n          message: `Cannot verify directory name '${dirName}': missing or invalid ${STANDARD_FILES.SKILL_MD} frontmatter`,\n        },\n      ];\n    }\n\n    return checkDirNameMatchesSkillId(frontmatter.name, skillMdRelPath, dirName);\n  } catch (error) {\n    return [\n      {\n        severity: \"warning\",\n        file: skillMdRelPath,\n        message: `Cannot verify directory name '${dirName}': ${getErrorMessage(error)}`,\n      },\n    ];\n  }\n}\n\n/**\n * Finds missing SKILL.md / metadata.yaml pairs (pure function, no I/O).\n *\n * Returns issues for:\n * - Directories with SKILL.md but no metadata.yaml\n * - Directories with metadata.yaml but no SKILL.md\n */\nexport function validateSkillFilePairs(\n  skillMdDirs: Set<string>,\n  metadataDirs: Set<string>,\n  skillsDir: string,\n): SourceValidationIssue[] {\n  const missingMetadata = [...skillMdDirs]\n    .filter((dir) => !metadataDirs.has(dir))\n    .map((dir) => ({\n      severity: \"error\" as const,\n      file: path.join(skillsDir, dir),\n      message: `Missing ${STANDARD_FILES.METADATA_YAML} — skill directory has ${STANDARD_FILES.SKILL_MD} but no metadata`,\n    }));\n\n  const missingSkillMd = [...metadataDirs]\n    .filter((dir) => !skillMdDirs.has(dir))\n    .map((dir) => ({\n      severity: \"error\" as const,\n      file: path.join(skillsDir, dir),\n      message: `Missing ${STANDARD_FILES.SKILL_MD} — skill directory has ${STANDARD_FILES.METADATA_YAML} but no SKILL.md`,\n    }));\n\n  return [...missingMetadata, ...missingSkillMd];\n}\n\n/**\n * Validates a skills source repository for metadata correctness.\n *\n * Checks:\n * 1. Every metadata.yaml against the strict validation schema\n *    (over-length cliDescription is downgraded to a warning)\n * 2. Directory name equals the skill's machine id (SKILL.md frontmatter name)\n * 3. Cross-references resolve to existing skill IDs (via checkMatrixHealth)\n * 4. camelCase key convention (no snake_case)\n * 5. Every skill directory has both SKILL.md and metadata.yaml\n */\nexport async function validateSource(sourcePath: string): Promise<SourceValidationResult> {\n  const issues: SourceValidationIssue[] = [];\n\n  const resolvedPath = path.isAbsolute(sourcePath) ? sourcePath : path.resolve(sourcePath);\n\n  if (!(await directoryExists(resolvedPath))) {\n    issues.push({\n      severity: \"error\",\n      file: resolvedPath,\n      message: \"Source directory does not exist\",\n    });\n    return buildResult(issues, 0);\n  }\n\n  const sourceProjectConfig = await loadProjectSourceConfig(resolvedPath);\n  const skillsDirRelPath = sourceProjectConfig?.skillsDir ?? SKILLS_DIR_PATH;\n  const skillsDir = path.join(resolvedPath, skillsDirRelPath);\n\n  if (!(await directoryExists(skillsDir))) {\n    issues.push({\n      severity: \"error\",\n      file: skillsDir,\n      message: \"Skills directory does not exist\",\n    });\n    return buildResult(issues, 0);\n  }\n\n  // Phase 1: Check every skill directory has both SKILL.md and metadata.yaml\n  const skillMdFiles = await glob(`**/${STANDARD_FILES.SKILL_MD}`, skillsDir);\n  const metadataFiles = await glob(`**/${STANDARD_FILES.METADATA_YAML}`, skillsDir);\n\n  const skillMdDirs = new Set(skillMdFiles.map((f) => path.dirname(f)));\n  const metadataDirs = new Set(metadataFiles.map((f) => path.dirname(f)));\n\n  issues.push(...validateSkillFilePairs(skillMdDirs, metadataDirs, skillsDir));\n\n  // Phase 2: Validate each metadata.yaml against strict schema and conventions.\n  // Pair violations were already reported by phase 1 — validate only complete pairs.\n  const validMetadataFiles = metadataFiles.filter((f) => skillMdDirs.has(path.dirname(f)));\n  for (const metadataFile of validMetadataFiles) {\n    issues.push(...(await validateOneSkill(skillsDir, skillsDirRelPath, metadataFile)));\n  }\n\n  // Phase 3: Cross-reference validation via matrix health check\n  issues.push(...(await checkCrossReferences(resolvedPath)));\n\n  // Phases 4–6: optional source-repo targets — run in parallel\n  // Phase 4: stack skill metadata + stack configs\n  // Phase 5: agent metadata\n  // Phase 6: config/*.ts runtime exports\n  const extraIssues = await Promise.all([\n    validateStacks(resolvedPath),\n    validateAgents(resolvedPath),\n    validateConfigFiles(resolvedPath),\n  ]);\n  issues.push(...extraIssues.flat());\n\n  return buildResult(issues, validMetadataFiles.length);\n}\n\n/**\n * One complete skill pair, judged four ways: its metadata.yaml parses, its keys are camelCase,\n * it satisfies the strict published-skill schema, and its directory is named after the id its\n * SKILL.md declares. A file nothing can be parsed out of reports that and stops — every check\n * after it reads the parsed value, so each would only restate the same fault.\n */\nasync function validateOneSkill(\n  skillsDir: string,\n  skillsDirRelPath: string,\n  metadataFile: string,\n): Promise<SourceValidationIssue[]> {\n  const relPath = path.join(skillsDirRelPath, metadataFile);\n\n  let rawMetadata: unknown;\n  try {\n    rawMetadata = parseYaml(await readFile(path.join(skillsDir, metadataFile)));\n  } catch (error) {\n    return [\n      {\n        severity: \"error\",\n        file: relPath,\n        message: `Failed to parse YAML: ${getErrorMessage(error)}`,\n      },\n    ];\n  }\n\n  return [\n    ...checkSnakeCaseKeys(rawMetadata, relPath),\n    ...checkMetadataSchema(rawMetadata, relPath),\n    // Independent of metadata validity — the id lives in SKILL.md frontmatter\n    ...(await checkSkillDirName(skillsDir, skillsDirRelPath, path.dirname(metadataFile))),\n  ];\n}\n\n/**\n * The strict published-skill schema's verdict, as its hard errors plus the one advisory\n * (over-length cliDescription) `splitMetadataValidationIssues` separates out.\n */\nfunction checkMetadataSchema(rawMetadata: unknown, relPath: string): SourceValidationIssue[] {\n  const result = validateSkillMetadata(rawMetadata);\n  if (result.success) return [];\n\n  const { errors, warnings } = splitMetadataValidationIssues(result.error, rawMetadata);\n  return [\n    ...errors.map((message) => ({ severity: \"error\" as const, file: relPath, message })),\n    ...warnings.map((message) => ({ severity: \"warning\" as const, file: relPath, message })),\n  ];\n}\n\n/**\n * Whether every relationship the source declares resolves to a skill it actually holds.\n * A source whose categories/rules could not be loaded is a warning rather than a failure: the\n * per-skill checks above already reported what they found, and this pass simply could not run.\n */\nasync function checkCrossReferences(resolvedPath: string): Promise<SourceValidationIssue[]> {\n  try {\n    await loadSkillsMatrixFromSource({ sourceFlag: resolvedPath, skipExtraSources: true });\n    return checkMatrixHealth(matrix).map((healthIssue) => ({\n      severity: healthIssue.severity,\n      file: SKILL_CATEGORIES_PATH,\n      message: healthIssue.details,\n    }));\n  } catch (error) {\n    return [\n      {\n        severity: \"warning\",\n        file: SKILL_CATEGORIES_PATH,\n        message: `Cross-reference validation skipped: failed to load categories/rules: ${getErrorMessage(error)}`,\n      },\n    ];\n  }\n}\n\n/**\n * Validates stack-embedded skill metadata.yaml files and stack config.yaml files.\n * Skips silently when src/stacks/ does not exist.\n */\nasync function validateStacks(resolvedPath: string): Promise<SourceValidationIssue[]> {\n  const stacksDir = path.join(resolvedPath, DIRS.stacks);\n  if (!(await directoryExists(stacksDir))) return [];\n\n  const [skillMetaIssues, configIssues] = await Promise.all([\n    validateYamlFiles({\n      baseDir: stacksDir,\n      relBaseDir: DIRS.stacks,\n      pattern: `**/skills/**/${STANDARD_FILES.METADATA_YAML}`,\n      schema: metadataValidationSchema,\n    }),\n    validateYamlFiles({\n      baseDir: stacksDir,\n      relBaseDir: DIRS.stacks,\n      pattern: `*/${STANDARD_FILES.CONFIG_YAML}`,\n      schema: stackConfigValidationSchema,\n    }),\n  ]);\n  return [...skillMetaIssues, ...configIssues];\n}\n\n/**\n * Validates agent metadata.yaml files against the compiled agent output schema.\n * Skips silently when src/agents/ does not exist.\n */\nasync function validateAgents(resolvedPath: string): Promise<SourceValidationIssue[]> {\n  const agentsDir = path.join(resolvedPath, DIRS.agents);\n  if (!(await directoryExists(agentsDir))) return [];\n\n  return validateYamlFiles({\n    baseDir: agentsDir,\n    relBaseDir: DIRS.agents,\n    pattern: `**/${STANDARD_FILES.AGENT_METADATA_YAML}`,\n    schema: agentYamlGenerationSchema,\n  });\n}\n\n/**\n * Validates TypeScript config files (skill-categories.ts, skill-rules.ts, stacks.ts)\n * by runtime-loading them via loadConfig and validating the default export.\n * Skips silently when a file does not exist.\n */\nasync function validateConfigFiles(resolvedPath: string): Promise<SourceValidationIssue[]> {\n  const results = await Promise.all([\n    validateTsConfig(resolvedPath, SKILL_CATEGORIES_PATH, skillCategoriesFileSchema),\n    validateTsConfig(resolvedPath, SKILL_RULES_PATH, skillRulesFileSchema),\n    validateTsConfig(resolvedPath, STACKS_FILE_PATH, stacksConfigSchema),\n  ]);\n  return results.flat();\n}\n\n/**\n * Globs YAML files under baseDir and validates each against the given schema.\n * Reports parse errors, schema errors (as field-path messages), and uses relBaseDir\n * for display paths so issue locations match the project-relative form used elsewhere.\n */\nasync function validateYamlFiles(opts: {\n  baseDir: string;\n  relBaseDir: string;\n  pattern: string;\n  schema: z.ZodType<unknown>;\n}): Promise<SourceValidationIssue[]> {\n  const issues: SourceValidationIssue[] = [];\n  const files = await glob(opts.pattern, opts.baseDir);\n\n  for (const relFile of files) {\n    const absPath = path.join(opts.baseDir, relFile);\n    const displayPath = path.join(opts.relBaseDir, relFile);\n\n    let parsed: unknown;\n    try {\n      parsed = parseYaml(await readFile(absPath));\n    } catch {\n      issues.push({ severity: \"error\", file: displayPath, message: \"Failed to parse YAML\" });\n      continue;\n    }\n\n    const result = opts.schema.safeParse(parsed);\n    if (result.success) continue;\n\n    issues.push(\n      ...formatZodErrors(result.error).map((message) => ({\n        severity: \"error\" as const,\n        file: displayPath,\n        message,\n      })),\n    );\n  }\n  return issues;\n}\n\n/**\n * Runtime-loads a TypeScript config file via loadConfig and reports validation failures.\n * Absent files are not errors — only report when the file exists but fails to load or validate.\n *\n * loadConfig already unwraps the default export (via jiti's `{ default: true }` + interopDefault),\n * so a returned `null` means the module has no default export (named-only modules surface here).\n */\nasync function validateTsConfig(\n  resolvedPath: string,\n  relConfigPath: string,\n  schema: z.ZodType<unknown>,\n): Promise<SourceValidationIssue[]> {\n  const absPath = path.join(resolvedPath, relConfigPath);\n  if (!(await fileExists(absPath))) return [];\n\n  try {\n    const loaded = await loadConfig(absPath, schema);\n    if (loaded === null) {\n      return [{ severity: \"error\", file: relConfigPath, message: \"Config has no default export\" }];\n    }\n    return [];\n  } catch (error) {\n    return [\n      { severity: \"error\", file: relConfigPath, message: formatLoadError(relConfigPath, error) },\n    ];\n  }\n}\n\n/**\n * Normalizes a loadConfig error so the message references the relative config path,\n * not the absolute path embedded by loadConfig's own template string.\n */\nfunction formatLoadError(relConfigPath: string, error: unknown): string {\n  const raw = getErrorMessage(error);\n  const stripped = raw.replace(/Failed to load config from '[^']+':\\s*/, \"\");\n  return `Failed to load ${relConfigPath}: ${stripped}`;\n}\n\nfunction buildResult(issues: SourceValidationIssue[], skillCount: number): SourceValidationResult {\n  const errorCount = issues.filter((i) => i.severity === \"error\").length;\n  const warningCount = issues.filter((i) => i.severity === \"warning\").length;\n  return { issues, skillCount, errorCount, warningCount };\n}\n","import os from \"os\";\nimport path from \"path\";\nimport { getErrorMessage } from \"../utils/errors.js\";\nimport { PLUGIN_MANIFEST_DIR, STANDARD_FILES } from \"../consts.js\";\nimport { directoryExists, fileExists, listDirectories } from \"../utils/fs.js\";\nimport { listAgentMdFiles } from \"./agents/index.js\";\nimport { readSkillMetadata } from \"./loading/index.js\";\nimport {\n  configDirsInPlay,\n  findConfigLoadFailures,\n  getProjectConfigPath,\n  isLocalSource,\n  resolvePrimarySourceEntry,\n  type ConfigLoadError,\n  type SourceEntry,\n} from \"./configuration/index.js\";\nimport { isHomeDirectory, resolveInstallPaths } from \"./installation/index.js\";\nimport {\n  getInstalledPluginsRegistryPath,\n  getProjectPluginsDir,\n  getUserPluginsDir,\n  listRegisteredPluginInstalls,\n  validateAgentFrontmatter,\n  validateAllPlugins,\n  validatePlugin,\n  validateSkillFrontmatter,\n  type ResolvedPlugin,\n} from \"./plugins/index.js\";\nimport { splitMetadataValidationIssues, validateSkillMetadata } from \"./schemas.js\";\nimport { isSourceRepo, validateSource } from \"./source-validator.js\";\nimport type { ValidationResult } from \"../types/index.js\";\n\n/** How a source repository under the cwd is labelled when it is not a registered source. */\nconst CWD_SOURCE_NAME = \"current directory\";\n\nexport type ContentIssue = {\n  severity: \"error\" | \"warning\";\n  /** The file or directory a reader has to open to fix the issue. */\n  file: string;\n  message: string;\n};\n\n/**\n * One content pass: what it walked, what it found, and what it deliberately did\n * not check. `notes` carries neither errors nor warnings — it is the record of\n * which sources were reached and which were skipped.\n */\nexport type ContentValidation = {\n  count: number;\n  issues: ContentIssue[];\n  notes: string[];\n};\n\nconst NOTHING_VALIDATED: ContentValidation = { count: 0, issues: [], notes: [] };\n\nfunction mergeValidations(parts: ContentValidation[]): ContentValidation {\n  return parts.reduce(\n    (acc, part) => ({\n      count: acc.count + part.count,\n      issues: [...acc.issues, ...part.issues],\n      notes: [...acc.notes, ...part.notes],\n    }),\n    NOTHING_VALIDATED,\n  );\n}\n\n/** Render an absolute path with a `~/` prefix when it's under the user's home directory. */\nfunction displayDir(absolutePath: string): string {\n  const home = os.homedir();\n  if (absolutePath === home) return \"~\";\n  if (absolutePath.startsWith(home + path.sep)) {\n    return `~${path.sep}${path.relative(home, absolutePath)}`;\n  }\n  return absolutePath;\n}\n\nfunction toIssues(file: string, result: ValidationResult): ContentIssue[] {\n  return [\n    ...result.errors.map((message) => ({ severity: \"error\" as const, file, message })),\n    ...result.warnings.map((message) => ({ severity: \"warning\" as const, file, message })),\n  ];\n}\n\n/** Says which of the three load outcomes a config file is in, without restating the loader. */\nconst CONFIG_UNREADABLE = \"exists but could not be loaded\";\n\n/**\n * Validates the config files this run reads: the project's own and the global one it inlines.\n *\n * A config that exists and cannot be parsed is reported here rather than left to the operational\n * layer, for the reason that layer exists to be gated on — every operational row is read OUT of\n * this file, so each would be a cascade of the same fault. It is also the only report that can\n * carry the loader's reason: the layers below re-read the file per check, and their own\n * diagnostics for it are what used to arrive spliced between the rows.\n *\n * An ABSENT config is not a finding here. It is the legitimate state `init` exists for, and the\n * operational layer already names it and offers the remedy that fits it.\n */\nexport async function validateProjectConfigFile(projectDir: string): Promise<ContentValidation> {\n  const [present, failures] = await Promise.all([\n    countExistingConfigs(projectDir),\n    findConfigLoadFailures(projectDir),\n  ]);\n\n  return { count: present, issues: failures.map(toUnreadableConfigIssue), notes: [] };\n}\n\nfunction toUnreadableConfigIssue(failure: ConfigLoadError): ContentIssue {\n  return {\n    severity: \"error\",\n    file: displayDir(failure.configPath),\n    message: `${CONFIG_UNREADABLE}: ${failure.reason}`,\n  };\n}\n\nasync function countExistingConfigs(projectDir: string): Promise<number> {\n  const present = await Promise.all(\n    configDirsInPlay(projectDir).map((dir) => fileExists(getProjectConfigPath(dir))),\n  );\n  return present.filter(Boolean).length;\n}\n\n/**\n * Validates the marketplace this installation reads from when it is local, plus the current\n * directory when that is itself a skills source repository — that repository is the content a\n * marketplace author runs this against, and it is not the source they read skills from (D-210).\n * A remote marketplace is recorded as skipped rather than fetched.\n */\nexport async function validateRegisteredSources(projectDir: string): Promise<ContentValidation> {\n  const primary = await resolvePrimarySourceEntry(projectDir);\n  const registered = [primary];\n  const remote = registered.filter((source) => !isLocalSource(source.url));\n  const local = await localSourcesToValidate(projectDir, registered);\n\n  const outcomes = await Promise.all(local.map(validateOneSource));\n\n  return {\n    count: local.length,\n    issues: outcomes.flatMap((outcome) => outcome.issues),\n    notes: [\n      ...outcomes.map((outcome) => outcome.note),\n      ...remote.map((source) => `${source.name} (${source.url}) — skipped (remote source)`),\n    ],\n  };\n}\n\nasync function localSourcesToValidate(\n  projectDir: string,\n  registered: SourceEntry[],\n): Promise<SourceEntry[]> {\n  const local = registered.filter((source) => isLocalSource(source.url));\n  const alreadyCovered = local.some(\n    (source) => path.resolve(projectDir, source.url) === projectDir,\n  );\n\n  if (alreadyCovered || !(await isSourceRepo(projectDir))) return local;\n\n  return [...local, { name: CWD_SOURCE_NAME, url: projectDir }];\n}\n\ntype SourceOutcome = { note: string; issues: ContentIssue[] };\n\nasync function validateOneSource(source: SourceEntry): Promise<SourceOutcome> {\n  const label = `${source.name} (${source.url})`;\n  try {\n    const result = await validateSource(source.url);\n    return { note: `${label} — ${result.skillCount} skills`, issues: result.issues };\n  } catch (error) {\n    return {\n      note: `${label} — failed`,\n      issues: [{ severity: \"error\", file: source.url, message: getErrorMessage(error) }],\n    };\n  }\n}\n\n/** Validates every installed plugin bundle in the global and project plugin directories. */\nexport async function validateInstalledPlugins(projectDir: string): Promise<ContentValidation> {\n  const dirs = [\n    getUserPluginsDir(),\n    ...(isHomeDirectory(projectDir) ? [] : [getProjectPluginsDir(projectDir)]),\n  ];\n  return mergeValidations(await Promise.all(dirs.map(validatePluginsDirectory)));\n}\n\nasync function validatePluginsDirectory(pluginsDir: string): Promise<ContentValidation> {\n  if (!(await directoryExists(pluginsDir))) return NOTHING_VALIDATED;\n\n  if (await fileExists(getInstalledPluginsRegistryPath(pluginsDir))) {\n    const registryValidation = await validateRegistryPlugins(pluginsDir);\n    if (registryValidation !== undefined) return registryValidation;\n  }\n\n  const pluginDirs = await findPluginDirectories(pluginsDir);\n  if (pluginDirs.length === 0) return NOTHING_VALIDATED;\n\n  const { results } = await validateAllPlugins(pluginsDir);\n\n  return {\n    count: results.length,\n    issues: results.flatMap(({ name, result }) => toIssues(name, result)),\n    notes: [],\n  };\n}\n\n/**\n * Validates the installs recorded in the plugins directory's `installed_plugins.json`\n * (claude CLI >=2.1.220 cache layout). Returns undefined when the registry records no\n * installs so the caller can fall back to the direct-children scan (older/manual layouts).\n */\nasync function validateRegistryPlugins(pluginsDir: string): Promise<ContentValidation | undefined> {\n  let installs: ResolvedPlugin[];\n  try {\n    installs = await listRegisteredPluginInstalls(pluginsDir);\n  } catch (error) {\n    return {\n      count: 0,\n      issues: [\n        {\n          severity: \"error\",\n          file: displayDir(getInstalledPluginsRegistryPath(pluginsDir)),\n          message: getErrorMessage(error),\n        },\n      ],\n      notes: [],\n    };\n  }\n\n  if (installs.length === 0) return undefined;\n\n  // A recorded installPath that no longer exists surfaces as an invalid plugin\n  // via validatePlugin's structure check, not a crash.\n  const results = await Promise.all(\n    installs.map(async ({ pluginKey, installPath }) =>\n      toIssues(pluginKey, await validatePlugin(installPath)),\n    ),\n  );\n\n  return { count: installs.length, issues: results.flat(), notes: [] };\n}\n\nasync function findPluginDirectories(pluginsDir: string): Promise<string[]> {\n  const entries = await listDirectories(pluginsDir);\n  const checks = await Promise.all(\n    entries.map(async (name) => ({\n      name,\n      isPlugin: await directoryExists(path.join(pluginsDir, name, PLUGIN_MANIFEST_DIR)),\n    })),\n  );\n  return checks.filter((check) => check.isPlugin).map((check) => check.name);\n}\n\n/** Validates the SKILL.md and metadata.yaml of every installed skill, both scopes. */\nexport async function validateInstalledSkills(projectDir: string): Promise<ContentValidation> {\n  return mergeValidations(\n    await Promise.all(installedDirs(projectDir, \"skillsDir\").map(validateSkillsDirectory)),\n  );\n}\n\n/** Validates the frontmatter of every compiled agent file, both scopes. */\nexport async function validateInstalledAgents(projectDir: string): Promise<ContentValidation> {\n  return mergeValidations(\n    await Promise.all(installedDirs(projectDir, \"agentsDir\").map(validateAgentsDirectory)),\n  );\n}\n\n/**\n * The directories to walk for an installed-content pass. At the home directory both\n * scopes resolve to the same place, so it is walked once instead of twice.\n */\nfunction installedDirs(projectDir: string, key: \"skillsDir\" | \"agentsDir\"): string[] {\n  const global = resolveInstallPaths(projectDir, \"global\")[key];\n  if (isHomeDirectory(projectDir)) return [global];\n  return [global, resolveInstallPaths(projectDir, \"project\")[key]];\n}\n\n/** What an installed-content pass walked, named rather than validated. */\nexport type InstalledArtifacts = {\n  /** Every installed skill directory, both scopes, as display paths. */\n  skills: string[];\n  /** Every compiled agent file, both scopes, as display paths. */\n  agents: string[];\n};\n\n/**\n * The same two walks {@link validateInstalledSkills} and {@link validateInstalledAgents} count,\n * listing what they found instead of judging it. `doctor` reports this when no configuration\n * exists to compare the installation against: there is nothing to validate the files AGAINST,\n * and naming them is the whole finding.\n */\nexport async function listInstalledArtifacts(projectDir: string): Promise<InstalledArtifacts> {\n  const [skills, agents] = await Promise.all([\n    listAcrossScopes(installedDirs(projectDir, \"skillsDir\"), listDirectories),\n    listAcrossScopes(installedDirs(projectDir, \"agentsDir\"), listAgentMdFiles),\n  ]);\n  return { skills, agents };\n}\n\nasync function listAcrossScopes(\n  dirs: string[],\n  listEntries: (dir: string) => Promise<string[]>,\n): Promise<string[]> {\n  const perDir = await Promise.all(dirs.map((dir) => listDisplayPaths(dir, listEntries)));\n  return perDir.flat();\n}\n\n/** One directory's entries as display paths, or nothing when the directory is absent. */\nasync function listDisplayPaths(\n  dir: string,\n  listEntries: (dir: string) => Promise<string[]>,\n): Promise<string[]> {\n  if (!(await directoryExists(dir))) return [];\n  const entries = await listEntries(dir);\n  return entries.map((entry) => displayDir(path.join(dir, entry)));\n}\n\nasync function validateSkillsDirectory(skillsDir: string): Promise<ContentValidation> {\n  if (!(await directoryExists(skillsDir))) return NOTHING_VALIDATED;\n\n  const skillDirs = await listDirectories(skillsDir);\n  if (skillDirs.length === 0) return NOTHING_VALIDATED;\n\n  const results = await Promise.all(\n    skillDirs.map(async (name) => {\n      const skillDir = path.join(skillsDir, name);\n      return toIssues(displayDir(skillDir), await validateInstalledSkill(skillDir));\n    }),\n  );\n\n  return { count: skillDirs.length, issues: results.flat(), notes: [] };\n}\n\nasync function validateAgentsDirectory(agentsDir: string): Promise<ContentValidation> {\n  if (!(await directoryExists(agentsDir))) return NOTHING_VALIDATED;\n\n  const agentFiles = await listAgentMdFiles(agentsDir);\n  if (agentFiles.length === 0) return NOTHING_VALIDATED;\n\n  const results = await Promise.all(\n    agentFiles.map(async (fileName) => {\n      const agentPath = path.join(agentsDir, fileName);\n      return toIssues(displayDir(agentPath), await validateAgentFrontmatter(agentPath));\n    }),\n  );\n\n  return { count: agentFiles.length, issues: results.flat(), notes: [] };\n}\n\nasync function validateInstalledSkill(skillDir: string): Promise<ValidationResult> {\n  const skillMdPath = path.join(skillDir, STANDARD_FILES.SKILL_MD);\n  const metadataPath = path.join(skillDir, STANDARD_FILES.METADATA_YAML);\n  const errors: string[] = [];\n  const warnings: string[] = [];\n\n  if (!(await fileExists(skillMdPath))) {\n    errors.push(`Missing ${STANDARD_FILES.SKILL_MD}`);\n  } else {\n    const frontmatterResult = await validateSkillFrontmatter(skillMdPath);\n    errors.push(...frontmatterResult.errors);\n    warnings.push(...frontmatterResult.warnings);\n  }\n\n  if (!(await fileExists(metadataPath))) {\n    errors.push(`Missing ${STANDARD_FILES.METADATA_YAML}`);\n  } else {\n    const metadataResult = await validateInstalledSkillMetadata(metadataPath);\n    errors.push(...metadataResult.errors);\n    warnings.push(...metadataResult.warnings);\n  }\n\n  return { valid: errors.length === 0, errors, warnings };\n}\n\nasync function validateInstalledSkillMetadata(metadataPath: string): Promise<ValidationResult> {\n  // Same judgment `compile` refuses on and local-skill discovery skips on: a file\n  // that describes no skill is reported here as the error it is. 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