agents-inc 0.149.1 → 0.150.0

package/dist/commands/doctor.js

@@ -0,0 +1,475 @@
+#!/usr/bin/env node
+import {
+  detectProject,
+  loadSource
+} from "../chunk-DDG4F3FE.js";
+import "../chunk-N4IZ6GBO.js";
+import "../chunk-CDMHSHBN.js";
+import "../chunk-VIFZ6NFH.js";
+import {
+  filterExcludedEntries,
+  listAgentMdFiles
+} from "../chunk-YKKIJHZB.js";
+import {
+  BaseCommand,
+  EXIT_CODES
+} from "../chunk-OA5SUEQD.js";
+import "../chunk-SYUOXSPU.js";
+import "../chunk-P3PN5SVI.js";
+import {
+  discoverLocalSkills,
+  effectivelyExcludedSkillIds,
+  getStackSkillIds,
+  getVerifiedPluginInstallPaths,
+  installBaseDir,
+  isHomeDirectory,
+  parseMarketplacePluginRef,
+  resolveInstallPaths,
+  validateProjectConfig
+} from "../chunk-KH7MOIM5.js";
+import {
+  directoryExists,
+  fileExists,
+  getErrorMessage,
+  setVerbose
+} from "../chunk-3LIU2ZEF.js";
+import {
+  matrix
+} from "../chunk-DJAZE4PD.js";
+import "../chunk-VEP23B5W.js";
+import {
+  CLAUDE_SRC_DIR,
+  CLI_INVOKE_COMMAND,
+  DEFAULT_BRANDING,
+  EJECT_SOURCE,
+  LOCAL_SKILLS_PATH,
+  STANDARD_FILES,
+  UI_SYMBOLS
+} from "../chunk-O5ASLZ2K.js";
+import "../chunk-YU2VGX5R.js";
+import {
+  init_esm_shims
+} from "../chunk-P56WJ5FA.js";
+
+// src/cli/commands/doctor.ts
+init_esm_shims();
+import os from "os";
+import path from "path";
+import { countBy, unique } from "remeda";
+var CONFIG_TS_REL = `${CLAUDE_SRC_DIR}/${STANDARD_FILES.CONFIG_TS}`;
+function checkConfigValid(config) {
+  if (!config) {
+    return {
+      result: {
+        kind: "config",
+        status: "fail",
+        message: `${CONFIG_TS_REL} not found`,
+        details: [`Run '${CLI_INVOKE_COMMAND} init' to create a configuration`]
+      },
+      config: null
+    };
+  }
+  const validation = validateProjectConfig(config);
+  if (!validation.valid) {
+    return {
+      result: {
+        kind: "config",
+        status: "fail",
+        message: `${CONFIG_TS_REL} has errors`,
+        details: validation.errors
+      },
+      config: null
+    };
+  }
+  if (validation.warnings.length > 0) {
+    return {
+      result: {
+        kind: "config",
+        status: "warn",
+        message: `${CONFIG_TS_REL} has warnings`,
+        details: validation.warnings
+      },
+      config
+    };
+  }
+  return {
+    result: {
+      kind: "config",
+      status: "pass",
+      message: `${CONFIG_TS_REL} is valid`
+    },
+    config
+  };
+}
+async function checkSkillsResolved(config, matrix2, projectDir) {
+  const excludedIds = effectivelyExcludedSkillIds(config.skills);
+  const stackIds = config.stack ? getStackSkillIds(config.stack) : [];
+  const uniqueSkills = unique([...stackIds, ...config.skills.map((s) => s.id)]).filter(
+    (id) => !excludedIds.has(id)
+  );
+  if (uniqueSkills.length === 0) {
+    return {
+      kind: "skills",
+      status: "pass",
+      message: "No skills configured"
+    };
+  }
+  const [localResult, globalResult] = await Promise.all([
+    discoverLocalSkills(projectDir),
+    !isHomeDirectory(projectDir) ? discoverLocalSkills(os.homedir()) : null
+  ]);
+  const localSkillIds = /* @__PURE__ */ new Set([
+    ...localResult?.skills.map((s) => s.id) ?? [],
+    ...globalResult?.skills.map((s) => s.id) ?? []
+  ]);
+  const missingSkills = [];
+  for (const skillId of uniqueSkills) {
+    const inMatrix = skillId in matrix2.skills;
+    const inLocal = localSkillIds.has(skillId);
+    if (!inMatrix && !inLocal) {
+      missingSkills.push(skillId);
+    }
+  }
+  if (missingSkills.length > 0) {
+    return {
+      kind: "skills",
+      status: "fail",
+      message: `${uniqueSkills.length - missingSkills.length}/${uniqueSkills.length} skills found`,
+      details: missingSkills.map((s) => `- ${s} (not found)`)
+    };
+  }
+  return {
+    kind: "skills",
+    status: "pass",
+    message: `${uniqueSkills.length}/${uniqueSkills.length} skills found`
+  };
+}
+async function checkAgentsCompiled(config, projectDir) {
+  const agents = config.agents ?? [];
+  if (agents.length === 0) {
+    return {
+      kind: "agents",
+      status: "pass",
+      message: "No agents configured"
+    };
+  }
+  const projectAgentsDir = resolveInstallPaths(projectDir, "project").agentsDir;
+  const globalAgentsDir = resolveInstallPaths(projectDir, "global").agentsDir;
+  const agentChecks = await Promise.all(
+    agents.map(async (agent) => {
+      const agentsDir = agent.scope === "global" ? globalAgentsDir : projectAgentsDir;
+      const agentPath = path.join(agentsDir, `${agent.name}.md`);
+      return { name: agent.name, compiled: await fileExists(agentPath) };
+    })
+  );
+  const missingAgents = agentChecks.filter((c) => !c.compiled).map((c) => c.name);
+  if (missingAgents.length > 0) {
+    return {
+      kind: "agents",
+      status: "warn",
+      message: `${missingAgents.length} agent${missingAgents.length === 1 ? "" : "s"} need${missingAgents.length === 1 ? "s" : ""} recompilation`,
+      details: missingAgents.map((a) => `- ${a} (missing)`)
+    };
+  }
+  return {
+    kind: "agents",
+    status: "pass",
+    message: `${agents.length}/${agents.length} agents compiled`
+  };
+}
+async function checkNoOrphans(config, projectDir) {
+  const projectAgentsDir = resolveInstallPaths(projectDir, "project").agentsDir;
+  const globalAgentsDir = resolveInstallPaths(projectDir, "global").agentsDir;
+  const scopesShareAgentsDir = isHomeDirectory(projectDir);
+  const [projectExists, globalExists] = await Promise.all([
+    directoryExists(projectAgentsDir),
+    !scopesShareAgentsDir ? directoryExists(globalAgentsDir) : false
+  ]);
+  if (!projectExists && !globalExists) {
+    return {
+      kind: "orphans",
+      status: "pass",
+      message: "No agents directory"
+    };
+  }
+  const projectMdFiles = projectExists ? await listAgentMdFiles(projectAgentsDir) : [];
+  const globalMdFiles = globalExists ? await listAgentMdFiles(globalAgentsDir) : [];
+  const activeProjectAgents = new Set(
+    (config.agents ?? []).filter((a) => a.scope === "project" && !a.excluded).map((a) => a.name)
+  );
+  const knownGlobalAgents = new Set(
+    (config.agents ?? []).filter((a) => a.scope === "global").map((a) => a.name)
+  );
+  const knownProjectDirAgents = scopesShareAgentsDir ? /* @__PURE__ */ new Set([...activeProjectAgents, ...knownGlobalAgents]) : activeProjectAgents;
+  const orphanedFiles = [];
+  for (const file of projectMdFiles) {
+    const agentName = file.replace(/\.md$/, "");
+    if (!knownProjectDirAgents.has(agentName)) {
+      orphanedFiles.push(agentName);
+    }
+  }
+  for (const file of globalMdFiles) {
+    const agentName = file.replace(/\.md$/, "");
+    if (!knownGlobalAgents.has(agentName)) {
+      orphanedFiles.push(agentName);
+    }
+  }
+  if (orphanedFiles.length > 0) {
+    return {
+      kind: "orphans",
+      status: "warn",
+      message: `${orphanedFiles.length} orphaned agent file${orphanedFiles.length === 1 ? "" : "s"}`,
+      details: orphanedFiles.map((f) => `- ${f}.md (not in config)`)
+    };
+  }
+  return {
+    kind: "orphans",
+    status: "pass",
+    message: "No orphaned agent files"
+  };
+}
+async function checkSkillsInstalled(config, projectDir) {
+  const skills = config.skills ?? [];
+  const ejectSkills = skills.filter((s) => s.source === EJECT_SOURCE);
+  if (ejectSkills.length === 0) {
+    return {
+      kind: "installed",
+      status: "pass",
+      message: "No eject-mode skills configured"
+    };
+  }
+  const skillChecks = await Promise.all(
+    ejectSkills.map(async (skill) => {
+      const baseDir = installBaseDir(projectDir, skill.scope);
+      const skillMdPath = path.join(baseDir, LOCAL_SKILLS_PATH, skill.id, STANDARD_FILES.SKILL_MD);
+      return { id: skill.id, installed: await fileExists(skillMdPath) };
+    })
+  );
+  const missingSkills = skillChecks.filter((c) => !c.installed).map((c) => c.id);
+  if (missingSkills.length > 0) {
+    return {
+      kind: "installed",
+      status: "warn",
+      message: `${missingSkills.length} skill${missingSkills.length === 1 ? "" : "s"} missing from disk`,
+      details: missingSkills.map((s) => `- ${s} (not found in ${LOCAL_SKILLS_PATH}/)`)
+    };
+  }
+  return {
+    kind: "installed",
+    status: "pass",
+    message: `${ejectSkills.length}/${ejectSkills.length} eject-mode skills installed`
+  };
+}
+async function checkPluginSkillsInstalled(config, projectDir) {
+  const pluginSkills = config.skills.filter((s) => s.source !== EJECT_SOURCE);
+  if (pluginSkills.length === 0) {
+    return {
+      kind: "plugins",
+      status: "pass",
+      message: "No plugin-mode skills configured"
+    };
+  }
+  const baseDirs = unique(pluginSkills.map((s) => installBaseDir(projectDir, s.scope)));
+  const missingPerBaseDir = await Promise.all(
+    baseDirs.map(async (baseDir) => {
+      const installedIds = new Set(
+        (await getVerifiedPluginInstallPaths(baseDir)).map(
+          (plugin) => parseMarketplacePluginRef(plugin.pluginKey)
+        )
+      );
+      return pluginSkills.filter((skill) => installBaseDir(projectDir, skill.scope) === baseDir).filter((skill) => !installedIds.has(skill.id)).map((skill) => skill.id);
+    })
+  );
+  const missingSkills = missingPerBaseDir.flat();
+  if (missingSkills.length > 0) {
+    return {
+      kind: "plugins",
+      status: "warn",
+      message: `${missingSkills.length} skill${missingSkills.length === 1 ? "" : "s"} not installed as plugins`,
+      details: missingSkills.map((s) => `- ${s} (no enabled plugin found)`)
+    };
+  }
+  return {
+    kind: "plugins",
+    status: "pass",
+    message: `${pluginSkills.length}/${pluginSkills.length} plugin-mode skills installed`
+  };
+}
+async function checkSourceReachable(projectDir) {
+  try {
+    const { sourceResult: result } = await loadSource({
+      projectDir
+    });
+    const skillCount = Object.keys(matrix.skills).length;
+    const sourceLabel = result.isLocal ? "local" : "remote";
+    return {
+      kind: "source",
+      status: "pass",
+      message: `Connected to ${sourceLabel}: ${result.sourcePath}`,
+      details: [`${skillCount} skills available`]
+    };
+  } catch (error) {
+    const message = getErrorMessage(error);
+    return {
+      kind: "source",
+      status: "fail",
+      message: "Failed to load source",
+      details: [message]
+    };
+  }
+}
+var CHECK_WIDTH = 20;
+function formatCheckName(name) {
+  return name.padEnd(CHECK_WIDTH);
+}
+function formatStatus(status) {
+  switch (status) {
+    case "pass":
+      return UI_SYMBOLS.CHECK;
+    case "fail":
+      return UI_SYMBOLS.CROSS;
+    case "warn":
+      return "!";
+    case "skip":
+      return "-";
+    default: {
+      const _exhaustive = status;
+      return _exhaustive;
+    }
+  }
+}
+function formatCheckLine(name, result) {
+  const headerLine = `  ${formatCheckName(name)}${formatStatus(result.status)}  ${result.message}`;
+  const detailLines = (result.details ?? []).map(
+    (detail) => `  ${" ".repeat(CHECK_WIDTH)}   ${detail}`
+  );
+  return [headerLine, ...detailLines];
+}
+function formatSummary(results) {
+  const counts = countBy(results, (r) => r.status);
+  const plural = (n, word) => `${n} ${word}${n === 1 ? "" : "s"}`;
+  const parts = [
+    `${counts.pass ?? 0} passed`,
+    plural(counts.warn ?? 0, "warning"),
+    plural(counts.fail ?? 0, "error")
+  ];
+  return `  Summary: ${parts.join(", ")}`;
+}
+var TIPS = [
+  {
+    kind: "agents",
+    status: "warn",
+    tip: `  Tip: Run '${CLI_INVOKE_COMMAND} compile' to generate missing agent files`
+  },
+  {
+    kind: "config",
+    status: "fail",
+    tip: `  Tip: Run '${CLI_INVOKE_COMMAND} init' to create or fix configuration`
+  },
+  {
+    kind: "skills",
+    status: "fail",
+    tip: "  Tip: Check skill IDs in config match available skills"
+  },
+  {
+    kind: "installed",
+    status: "warn",
+    // No command is named on purpose: 'eject skills --force' re-copies every skill in the
+    // source and always targets project scope, so it cannot repair a global-scoped skill
+    // and it litters a plugin-mode project with local skill directories.
+    tip: "  Tip: Re-eject the missing skills from the source to restore their files"
+  }
+];
+function formatTips(results) {
+  return TIPS.filter((t) => results.some((r) => r.kind === t.kind && r.status === t.status)).map(
+    (t) => t.tip
+  );
+}
+function skippedResult(kind) {
+  return { kind, status: "skip", message: "Skipped (config invalid)" };
+}
+async function safeCheck(kind, fn) {
+  try {
+    return await fn();
+  } catch (error) {
+    return { kind, status: "fail", message: "Check threw", details: [getErrorMessage(error)] };
+  }
+}
+var Doctor = class _Doctor extends BaseCommand {
+  static summary = "Diagnose common configuration issues";
+  static description = `Run diagnostic checks on your ${DEFAULT_BRANDING.NAME} configuration to identify issues with config validity, skill resolution, agent compilation, and source connectivity.`;
+  static examples = ["<%= config.bin %> <%= command.id %>"];
+  // Override parent baseFlags to drop --source (not relevant for diagnostics)
+  static baseFlags = {};
+  static flags = {};
+  async run() {
+    await this.parse(_Doctor);
+    setVerbose(true);
+    const projectDir = process.cwd();
+    this.printHeader();
+    const results = await this.runAllChecks(projectDir);
+    this.printResults(results);
+    if (results.some((r) => r.status === "fail")) {
+      this.exit(EXIT_CODES.ERROR);
+    }
+  }
+  printHeader() {
+    this.log("");
+    this.log(`${DEFAULT_BRANDING.NAME} Doctor`);
+    this.log("");
+    this.log("  Checking configuration health...");
+    this.log("");
+  }
+  async runAllChecks(projectDir) {
+    const detected = await detectProject(projectDir);
+    const { result: configResult, config } = checkConfigValid(detected?.config ?? null);
+    this.logCheck("Config Valid", configResult);
+    const sourceResult = await safeCheck("source", () => checkSourceReachable(projectDir));
+    const filteredConfig = config ? filterExcludedEntries(config) : null;
+    const skillsResult = !config ? skippedResult("skills") : sourceResult.status === "fail" ? {
+      kind: "skills",
+      status: "skip",
+      message: "Skipped (source unreachable)"
+    } : await safeCheck("skills", () => checkSkillsResolved(config, matrix, projectDir));
+    this.logCheck("Skills Resolved", skillsResult);
+    const agentsResult = filteredConfig ? await safeCheck("agents", () => checkAgentsCompiled(filteredConfig, projectDir)) : skippedResult("agents");
+    this.logCheck("Agents Compiled", agentsResult);
+    const orphansResult = config ? await safeCheck("orphans", () => checkNoOrphans(config, projectDir)) : skippedResult("orphans");
+    this.logCheck("No Orphans", orphansResult);
+    const installedResult = filteredConfig ? await safeCheck("installed", () => checkSkillsInstalled(filteredConfig, projectDir)) : skippedResult("installed");
+    this.logCheck("Skills Installed", installedResult);
+    const pluginsResult = filteredConfig ? await safeCheck("plugins", () => checkPluginSkillsInstalled(filteredConfig, projectDir)) : skippedResult("plugins");
+    this.logCheck("Plugins Installed", pluginsResult);
+    this.logCheck("Source Reachable", sourceResult);
+    return [
+      configResult,
+      skillsResult,
+      agentsResult,
+      orphansResult,
+      installedResult,
+      pluginsResult,
+      sourceResult
+    ];
+  }
+  logCheck(name, result) {
+    for (const line of formatCheckLine(name, result)) {
+      this.log(line);
+    }
+  }
+  printResults(results) {
+    this.log("");
+    this.log(formatSummary(results));
+    const tips = formatTips(results);
+    if (tips.length > 0) {
+      this.log("");
+      for (const tip of tips) {
+        this.log(tip);
+      }
+    }
+    this.log("");
+  }
+};
+export {
+  Doctor as default
+};
+//# sourceMappingURL=doctor.js.map

package/dist/commands/doctor.js.map

@@ -0,0 +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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