agileflow 4.0.0-alpha.2 → 4.0.0-alpha.21

package/src/cli/commands/doctor.js

@@ -9,28 +9,126 @@
  * Exit code: 0 on green, 1 if any errors. Warnings are surfaced but
  * don't fail the command.
  */
-const path = require('path');
-const fs = require('fs');
+const path = require("path");
+const fs = require("fs");
 
-const { discoverPlugins } = require('../../runtime/plugins/registry.js');
+const { discoverPlugins } = require("../../runtime/plugins/registry.js");
 const {
   validatePluginSet,
   hasErrors: pluginHasErrors,
-} = require('../../runtime/plugins/validator.js');
-const {
-  loadHookManifest,
-} = require('../../runtime/hooks/manifest-loader.js');
-const {
-  buildHookManifest,
-} = require('../../runtime/hooks/aggregator.js');
-const { resolvePlugins } = require('../../runtime/plugins/resolver.js');
+} = require("../../runtime/plugins/validator.js");
+const { loadHookManifest } = require("../../runtime/hooks/manifest-loader.js");
+const { buildHookManifest } = require("../../runtime/hooks/aggregator.js");
+const { resolvePlugins } = require("../../runtime/plugins/resolver.js");
 const {
   validateSkillsAtRoot,
   validateSkill,
   loadSkill,
   detectKeywordCollisions,
   hasErrors: skillHasErrors,
-} = require('../../runtime/skills/validator.js');
+} = require("../../runtime/skills/validator.js");
+const { loadConfig } = require("../../runtime/config/loader.js");
+const { IDE_CAPABILITIES } = require("../../runtime/ide/capabilities.js");
+const {
+  MANAGED_EVENTS,
+  LEGACY_MANAGED_EVENTS,
+  HOOK_COMMAND_MARKER,
+  isAgileflowEntry,
+} = require("../../runtime/ide/claude-code-settings.js");
+
+/**
+ * v3-era directories under `.agileflow/` that v4 never writes.
+ * Detection-only — actual removal is the follow-up `--fix` work.
+ */
+const LEGACY_AGILEFLOW_SUBDIRS = [
+  "agents",
+  "base-prompts",
+  "cache",
+  "commands",
+  "config",
+  "council",
+  "experts",
+  "hooks",
+  "knowledge",
+  "lib",
+  "mixins",
+  "profiles",
+  "scripts",
+  "snippets",
+];
+
+/** v3-era files at `.agileflow/` root that v4 doesn't write. */
+const LEGACY_AGILEFLOW_FILES = ["CHANGELOG.md", "config.yaml"];
+
+/**
+ * v3-era directories under `.claude/` that v4 doesn't populate.
+ * `agents/` and `commands/` are intentionally NOT here — v4 still
+ * mirrors plugin slash-commands and subagents into them via
+ * claude-code-content.js. Only flagged if they contain agileflow-*
+ * entries (see section C below).
+ */
+const LEGACY_CLAUDE_SUBDIRS = ["hooks", "plans"];
+
+/** Narrow a value to a plain object (not array, not null, not primitive). */
+function isPlainObject(v) {
+  return v != null && typeof v === "object" && !Array.isArray(v);
+}
+
+/**
+ * Read JSON file, returning null on any failure (missing, malformed,
+ * permission denied). The detector treats unreadable config as "skip
+ * this section" rather than crashing.
+ */
+function readJSONSafe(p) {
+  try {
+    return JSON.parse(fs.readFileSync(p, "utf8"));
+  } catch {
+    return null;
+  }
+}
+
+/** readdirSync wrapped to return [] on permission-denied / vanished dirs. */
+function readdirSafe(p) {
+  try {
+    return fs.readdirSync(p);
+  } catch {
+    return [];
+  }
+}
+
+/**
+ * Expand env vars and ~ in a hook command's script path, then check if
+ * that file exists. Returns the resolved path if it's broken (file
+ * referenced but doesn't exist), or null otherwise (no path, or path
+ * exists, or path is opaque).
+ *
+ * Recognizes paths ending in common script extensions; conservative on
+ * purpose so we don't false-positive on shell builtins or commands
+ * that just happen to have a slash.
+ *
+ * @param {string} command
+ * @param {string} cwd
+ * @returns {string|null}
+ */
+function brokenScriptInCommand(command, cwd) {
+  if (typeof command !== "string") return null;
+  // Skip our own dispatcher — handled by other detection kinds.
+  if (command.includes(HOOK_COMMAND_MARKER)) return null;
+  // Extract path-like tokens with a known script extension.
+  const tokens = command.match(
+    /[\w$~/.\-\\]+\.(?:js|sh|py|ts|mjs|cjs|bash|zsh|rb)\b/g,
+  );
+  if (!tokens) return null;
+  for (const tok of tokens) {
+    let p = tok
+      .replace(/\$CLAUDE_PROJECT_DIR/g, cwd)
+      .replace(/\$HOME/g, require("os").homedir())
+      .replace(/^~(?=\/|$)/, require("os").homedir());
+    if (!path.isAbsolute(p)) p = path.join(cwd, p);
+    if (!fs.existsSync(p)) return p;
+  }
+  return null;
+}
 
 /**
  * Walk `content/plugins/<plugin>/skills/<skill>/SKILL.md` for every
@@ -43,7 +141,7 @@ async function validateBundledSkills() {
   /** @type {Array<import('../../runtime/skills/validator.js').SkillManifest>} */
   const allSkills = [];
   for (const p of plugins) {
-    const root = path.join(p.dir, 'skills');
+    const root = path.join(p.dir, "skills");
     const r = await validateSkillsAtRoot(root);
     issues.push(...r.issues);
     allSkills.push(...r.skills);
@@ -65,7 +163,9 @@ async function validateAggregatedHookManifest() {
     const plugins = discoverPlugins();
     const { ordered } = resolvePlugins(plugins, []);
     const manifestObj = buildHookManifest(ordered);
-    const { normalizeManifest } = require('../../runtime/hooks/manifest-loader.js');
+    const {
+      normalizeManifest,
+    } = require("../../runtime/hooks/manifest-loader.js");
     normalizeManifest(manifestObj);
   } catch (err) {
     errors.push(err.message);
@@ -77,7 +177,7 @@ async function validateAggregatedHookManifest() {
  * Validate a project's installed hook manifest file (if present).
  */
 async function validateInstalledManifest(cwd) {
-  const manifestPath = path.join(cwd, '.agileflow', 'hook-manifest.yaml');
+  const manifestPath = path.join(cwd, ".agileflow", "hook-manifest.yaml");
   if (!fs.existsSync(manifestPath)) return [];
   /** @type {string[]} */
   const errors = [];
@@ -101,54 +201,739 @@ function printSection(title, issues) {
   console.log(`\n${title}`);
   if (issues.length === 0) {
     // eslint-disable-next-line no-console
-    console.log('  ok');
+    console.log("  ok");
     return 0;
   }
   let errorCount = 0;
   for (const issue of issues) {
-    const sev = issue.severity || 'error';
-    if (sev === 'error') errorCount += 1;
-    const label = sev === 'error' ? 'ERROR' : 'WARN ';
-    const id = issue.skillId || issue.pluginId || '';
-    const idPrefix = id ? `[${id}] ` : '';
+    const sev = issue.severity || "error";
+    if (sev === "error") errorCount += 1;
+    const label = sev === "error" ? "ERROR" : "WARN ";
+    const id = issue.skillId || issue.pluginId || "";
+    const idPrefix = id ? `[${id}] ` : "";
     // eslint-disable-next-line no-console
     console.log(`  ${label} ${idPrefix}${issue.message}`);
   }
   return errorCount;
 }
 
-async function doctor() {
+/**
+ * Check installation health in the current project directory.
+ * Returns issues describing missing/misconfigured IDE setup.
+ */
+async function checkInstallHealth(cwd) {
+  const issues = [];
+  const configPath = path.join(cwd, "agileflow.config.json");
+
+  if (!fs.existsSync(configPath)) {
+    issues.push({
+      severity: "warn",
+      message:
+        "agileflow.config.json not found — run `agileflow setup` to configure",
+    });
+    return issues;
+  }
+
+  let cfg;
+  try {
+    cfg = JSON.parse(fs.readFileSync(configPath, "utf8"));
+  } catch {
+    issues.push({
+      severity: "error",
+      message: "agileflow.config.json is not valid JSON",
+    });
+    return issues;
+  }
+
+  const targets = cfg?.ide?.targets;
+  if (!Array.isArray(targets) || targets.length === 0) {
+    issues.push({
+      severity: "warn",
+      message: "No IDE targets configured in agileflow.config.json",
+    });
+    return issues;
+  }
+
+  for (const ide of targets) {
+    const caps = IDE_CAPABILITIES[ide];
+    if (!caps) {
+      issues.push({
+        severity: "warn",
+        message: `Unknown IDE target "${ide}" in config`,
+      });
+      continue;
+    }
+
+    // Check skills directory exists and has at least one SKILL.md
+    if (caps.skills) {
+      const skillsDir = path.join(cwd, caps.skillsDir);
+      if (!fs.existsSync(skillsDir)) {
+        issues.push({
+          severity: "warn",
+          message: `[${ide}] Skills not installed — ${caps.skillsDir}/ missing. Run \`agileflow setup\``,
+        });
+      } else {
+        const skillFiles = fs.readdirSync(skillsDir).filter((f) => {
+          const skillPath = path.join(skillsDir, f, "SKILL.md");
+          return fs.existsSync(skillPath);
+        });
+        if (skillFiles.length === 0) {
+          issues.push({
+            severity: "error",
+            message: `[${ide}] Skills directory exists but contains no SKILL.md files`,
+          });
+        } else {
+          issues.push({
+            severity: "info",
+            message: `[${ide}] ${skillFiles.length} skill(s) installed in ${caps.skillsDir}/`,
+          });
+        }
+      }
+    }
+
+    // Check hooks wired in IDE settings
+    if (caps.hooks && caps.settingsFile) {
+      const settingsPath = path.join(cwd, caps.settingsFile);
+      if (!fs.existsSync(settingsPath)) {
+        issues.push({
+          severity: "warn",
+          message: `[${ide}] Settings file not found at ${caps.settingsFile} — hooks may not fire`,
+        });
+      } else {
+        try {
+          const settings = JSON.parse(fs.readFileSync(settingsPath, "utf8"));
+          const hasHooks =
+            settings?.hooks && Object.keys(settings.hooks).length > 0;
+          if (!hasHooks) {
+            issues.push({
+              severity: "warn",
+              message: `[${ide}] No hooks found in ${caps.settingsFile} — SessionStart injection unavailable`,
+            });
+          } else {
+            const hookEvents = Object.keys(settings.hooks);
+            issues.push({
+              severity: "info",
+              message: `[${ide}] Hooks wired: ${hookEvents
+                .filter((e) => !LEGACY_MANAGED_EVENTS.has(e))
+                .join(", ")}`,
+            });
+          }
+        } catch {
+          issues.push({
+            severity: "warn",
+            message: `[${ide}] Could not parse ${caps.settingsFile}`,
+          });
+        }
+      }
+    }
+  }
+
+  return issues;
+}
+
+/**
+ * Build the shared input bundle every detector / fixer needs. Reading
+ * once here avoids the duplicate settings.json parse the old monolith
+ * did (once for hook-event detection, once for broken-command).
+ *
+ * @param {string} cwd
+ * @returns {{
+ *   cwd: string,
+ *   settingsPath: string,
+ *   settings: any,
+ *   agileflowDir: string,
+ *   claudeDir: string,
+ *   configPath: string,
+ *   config: any,
+ *   manifestPath: string,
+ * }}
+ */
+function buildContext(cwd) {
+  const settingsPath = path.join(cwd, ".claude", "settings.json");
+  const configPath = path.join(cwd, "agileflow.config.json");
+  return {
+    cwd,
+    settingsPath,
+    settings: fs.existsSync(settingsPath) ? readJSONSafe(settingsPath) : null,
+    agileflowDir: path.join(cwd, ".agileflow"),
+    claudeDir: path.join(cwd, ".claude"),
+    configPath,
+    config: fs.existsSync(configPath) ? readJSONSafe(configPath) : null,
+    manifestPath: path.join(cwd, ".agileflow", "hook-manifest.yaml"),
+  };
+}
+
+/**
+ * Walk `.claude/settings.json` hooks, coerce malformed shapes, and yield
+ * `[event, entries]` pairs every hook-related detector / fixer iterates.
+ * Returns [] when settings or hooks are missing / wrong-shape.
+ *
+ * @param {any} settings
+ * @returns {Array<[string, Array<any>]>}
+ */
+function iterHookEvents(settings) {
+  if (!settings || !isPlainObject(settings.hooks)) return [];
+  return Object.keys(settings.hooks).map((event) => {
+    const raw = settings.hooks[event];
+    let entries;
+    if (Array.isArray(raw)) entries = raw;
+    else if (isPlainObject(raw)) entries = [raw];
+    else entries = [];
+    return [event, entries];
+  });
+}
+
+/** (A) Legacy / orphan hook events — AgileFlow entries in events we no longer manage. */
+function detectLegacyHookEvents(ctx) {
+  const issues = [];
+  for (const [event, entries] of iterHookEvents(ctx.settings)) {
+    const ours = entries.filter(isAgileflowEntry);
+    if (ours.length === 0) continue;
+    if (LEGACY_MANAGED_EVENTS.has(event)) {
+      issues.push({
+        severity: "warn",
+        kind: "legacy-hook-event",
+        path: `${ctx.settingsPath}#hooks.${event}`,
+        message: `Legacy hook event "${event}" in .claude/settings.json — AgileFlow used to write this, no longer does. Safe to remove ${ours.length} entry/entries.`,
+      });
+    } else if (!MANAGED_EVENTS.has(event)) {
+      issues.push({
+        severity: "warn",
+        kind: "orphan-hook-event",
+        path: `${ctx.settingsPath}#hooks.${event}`,
+        message: `Unknown event "${event}" in .claude/settings.json contains \`${HOOK_COMMAND_MARKER}\` command — not a current AgileFlow event. Probably from a much older install.`,
+      });
+    }
+  }
+  return issues;
+}
+
+/** (F) Broken hook commands — entries whose `command` references a missing file. */
+function detectBrokenHookCommands(ctx) {
+  const issues = [];
+  for (const [event, entries] of iterHookEvents(ctx.settings)) {
+    for (const entry of entries) {
+      if (!entry || !Array.isArray(entry.hooks)) continue;
+      for (const h of entry.hooks) {
+        if (!h || h.type !== "command" || typeof h.command !== "string") {
+          continue;
+        }
+        const missingPath = brokenScriptInCommand(h.command, ctx.cwd);
+        if (!missingPath) continue;
+        issues.push({
+          severity: "error",
+          kind: "broken-hook-command",
+          path: `${ctx.settingsPath}#hooks.${event}`,
+          event,
+          command: h.command,
+          missingPath,
+          message: `Hook in .claude/settings.json#hooks.${event} references missing file: ${missingPath} (command: \`${h.command}\`)`,
+        });
+      }
+    }
+  }
+  return issues;
+}
+
+/** (B) v3-era directories and files under `.agileflow/`. */
+function detectLegacyAgileflowPaths(ctx) {
+  const issues = [];
+  if (!fs.existsSync(ctx.agileflowDir)) return issues;
+  for (const name of LEGACY_AGILEFLOW_SUBDIRS) {
+    const p = path.join(ctx.agileflowDir, name);
+    if (fs.existsSync(p)) {
+      issues.push({
+        severity: "warn",
+        kind: "legacy-agileflow-subdir",
+        path: p,
+        message: `v3 directory \`.agileflow/${name}/\` present — v4 (skills-first) doesn't use this. Safe to delete unless you've kept custom content.`,
+      });
+    }
+  }
+  for (const name of LEGACY_AGILEFLOW_FILES) {
+    const p = path.join(ctx.agileflowDir, name);
+    if (fs.existsSync(p)) {
+      issues.push({
+        severity: "warn",
+        kind: "legacy-agileflow-file",
+        path: p,
+        message: `v3 file \`.agileflow/${name}\` present — not written by v4.`,
+      });
+    }
+  }
+  return issues;
+}
+
+/** (C) v3-era directories under `.claude/` — flagged only if they hold agileflow-* entries. */
+function detectLegacyClaudeSubdirs(ctx) {
+  const issues = [];
+  if (!fs.existsSync(ctx.claudeDir)) return issues;
+  for (const name of LEGACY_CLAUDE_SUBDIRS) {
+    const p = path.join(ctx.claudeDir, name);
+    if (!fs.existsSync(p)) continue;
+    const agileflowOwned = readdirSafe(p).filter(
+      (e) => e.startsWith("agileflow") || e.startsWith("AgileFlow"),
+    );
+    if (agileflowOwned.length === 0) continue;
+    issues.push({
+      severity: "warn",
+      kind: "legacy-claude-subdir",
+      path: p,
+      message: `v3 \`.claude/${name}/\` contains ${agileflowOwned.length} AgileFlow item(s) — v4 ships skills only; this dir isn't used.`,
+    });
+  }
+  return issues;
+}
+
+/**
+ * (D) Broken hook-manifest script references. YAML parse failures fall
+ * through silently — they're reported separately by
+ * `validateInstalledManifest()`, so we just skip the walk on parse fail.
+ */
+async function detectBrokenHookScripts(ctx) {
+  const issues = [];
+  if (!fs.existsSync(ctx.manifestPath)) return issues;
+  /** @type {{ hooks?: Array<{id: string, event: string, script: string}> } | null} */
+  let manifest = null;
+  try {
+    manifest = await loadHookManifest(ctx.manifestPath);
+  } catch {
+    return issues;
+  }
+  if (!manifest || !Array.isArray(manifest.hooks)) return issues;
+  for (const h of manifest.hooks) {
+    if (!h || typeof h.script !== "string") continue;
+    const scriptPath = path.isAbsolute(h.script)
+      ? h.script
+      : path.join(ctx.cwd, h.script);
+    if (!fs.existsSync(scriptPath)) {
+      issues.push({
+        severity: "error",
+        kind: "broken-hook-script",
+        path: scriptPath,
+        message: `Hook "${h.id}" (${h.event}) points at missing script ${h.script}`,
+      });
+    }
+  }
+  return issues;
+}
+
+/** (E) Orphan skill dirs — installed agileflow-* skills not claimed by an enabled plugin. */
+async function detectOrphanSkillDirs(ctx) {
+  const issues = [];
+  // Guard against malformed plugins fields: string, array, primitive.
+  // Object.entries on a string returns char-indexed entries; on an
+  // array it returns numeric-indexed ones — both produce garbage.
+  if (!ctx.config || !isPlainObject(ctx.config.plugins)) return issues;
+  const enabled = Object.entries(ctx.config.plugins)
+    .filter(([, v]) => v && v.enabled !== false)
+    .map(([k]) => k);
+  // De-dupe: don't push "core" if config already has it enabled.
+  if (!enabled.includes("core")) enabled.push("core");
+  /** @type {Set<string>} */
+  const expectedSkillIds = new Set();
+  for (const p of discoverPlugins()) {
+    if (!enabled.includes(p.id)) continue;
+    const skillsRoot = path.join(p.dir, "skills");
+    if (!fs.existsSync(skillsRoot)) continue;
+    for (const entry of readdirSafe(skillsRoot)) {
+      const skillFile = path.join(skillsRoot, entry, "SKILL.md");
+      if (!fs.existsSync(skillFile)) continue;
+      // loadSkill returns { skillId, frontmatter, body, ... } or throws.
+      // Either way, claim the dir name so we don't false-positive on a
+      // bundled skill.
+      let id = entry;
+      try {
+        const s = await loadSkill(skillFile);
+        id = (s && s.frontmatter && s.frontmatter.name) || s.skillId || entry;
+      } catch {
+        // unparseable bundled skill — still treat dir as owned
+      }
+      expectedSkillIds.add(id);
+    }
+  }
+  const skillsDir = path.join(ctx.claudeDir, "skills");
+  if (!fs.existsSync(skillsDir)) return issues;
+  for (const entry of readdirSafe(skillsDir)) {
+    if (!entry.startsWith("agileflow")) continue;
+    if (expectedSkillIds.has(entry)) continue;
+    issues.push({
+      severity: "warn",
+      kind: "orphan-skill-dir",
+      path: path.join(skillsDir, entry),
+      message: `Orphan skill \`.claude/skills/${entry}/\` — not owned by any enabled plugin. Likely from a disabled or removed plugin.`,
+    });
+  }
+  return issues;
+}
+
+/**
+ * Parse a `<settingsPath>#hooks.<event>` issue.path. Returns null if
+ * the marker is missing.
+ *
+ * @param {string} issuePath
+ * @returns {{settingsPath: string, event: string} | null}
+ */
+function parseHookEventPath(issuePath) {
+  const hashIdx = (issuePath || "").lastIndexOf("#hooks.");
+  if (hashIdx < 0) return null;
+  return {
+    settingsPath: issuePath.slice(0, hashIdx),
+    event: issuePath.slice(hashIdx + "#hooks.".length),
+  };
+}
+
+/**
+ * Persist a filtered hooks object back to settings.json, deleting the
+ * event entirely if no entries remain and dropping the hooks key if
+ * empty. Returns the relative .claude/settings.json#hooks.<event>
+ * string for use in success messages.
+ */
+function writeFilteredHooks(settings, settingsPath, event, kept) {
+  if (kept.length === 0) delete settings.hooks[event];
+  else settings.hooks[event] = kept;
+  if (Object.keys(settings.hooks).length === 0) delete settings.hooks;
+  fs.writeFileSync(settingsPath, JSON.stringify(settings, null, 2) + "\n");
+}
+
+/** Fix: strip AgileFlow entries from a hook event, preserving user entries. */
+function fixHookEventEntry(issue) {
+  const parsed = parseHookEventPath(issue.path);
+  if (!parsed) {
+    return {
+      ok: false,
+      message: "Malformed issue.path; expected #hooks.<event>",
+    };
+  }
+  const { settingsPath, event } = parsed;
+  const settings = readJSONSafe(settingsPath);
+  if (!settings || !isPlainObject(settings.hooks)) {
+    return { ok: false, message: `No hooks object in ${settingsPath}` };
+  }
+  const raw = settings.hooks[event];
+  const entries = Array.isArray(raw) ? raw : isPlainObject(raw) ? [raw] : [];
+  const userEntries = entries.filter((e) => !isAgileflowEntry(e));
+  writeFilteredHooks(settings, settingsPath, event, userEntries);
+  return {
+    ok: true,
+    message: `Removed AgileFlow entries from .claude/settings.json#hooks.${event}`,
+  };
+}
+
+/** Fix: recursively remove a directory artifact. */
+function fixDirectoryRemoval(issue, ctx) {
+  if (!issue.path || !fs.existsSync(issue.path)) {
+    return { ok: false, message: `Path missing: ${issue.path}` };
+  }
+  fs.rmSync(issue.path, { recursive: true, force: true });
+  return { ok: true, message: `Removed ${path.relative(ctx.cwd, issue.path)}` };
+}
+
+/** Fix: unlink a file artifact. */
+function fixFileRemoval(issue, ctx) {
+  if (!issue.path || !fs.existsSync(issue.path)) {
+    return { ok: false, message: `Path missing: ${issue.path}` };
+  }
+  fs.unlinkSync(issue.path);
+  return { ok: true, message: `Removed ${path.relative(ctx.cwd, issue.path)}` };
+}
+
+/**
+ * Fix: delete agileflow-* children of a legacy .claude/ subdir, leaving
+ * user files alone. Empty parent dir is cleaned up best-effort.
+ */
+function fixClaudeSubdirSelective(issue, ctx) {
+  if (!issue.path || !fs.existsSync(issue.path)) {
+    return { ok: false, message: `Path missing: ${issue.path}` };
+  }
+  let removed = 0;
+  for (const entry of readdirSafe(issue.path)) {
+    if (!entry.startsWith("agileflow") && !entry.startsWith("AgileFlow"))
+      continue;
+    const p = path.join(issue.path, entry);
+    fs.rmSync(p, { recursive: true, force: true });
+    removed += 1;
+  }
+  // Empty-dir cleanup — fail silently if dir has other content.
+  try {
+    fs.rmdirSync(issue.path);
+  } catch {
+    /* dir not empty (user files present); leave it */
+  }
+  return {
+    ok: true,
+    message: `Removed ${removed} AgileFlow item(s) from ${path.relative(ctx.cwd, issue.path)}`,
+  };
+}
+
+/** Fix: broken hook script — not auto-fixable; the script file itself is gone. */
+function fixBrokenHookScriptStub() {
+  return {
+    ok: false,
+    message:
+      "Cannot auto-fix — the script file is gone. Run `agileflow update` to reinstall plugin scripts.",
+  };
+}
+
+/** Fix: strip a hook entry whose command matches a missing path, preserving siblings. */
+function fixBrokenHookCommand(issue) {
+  const parsed = parseHookEventPath(issue.path);
+  if (!parsed || !issue.command) {
+    return {
+      ok: false,
+      message: "Malformed issue — expected path and command",
+    };
+  }
+  const { settingsPath, event } = parsed;
+  const settings = readJSONSafe(settingsPath);
+  if (!settings || !isPlainObject(settings.hooks)) {
+    return { ok: false, message: `No hooks object in ${settingsPath}` };
+  }
+  const raw = settings.hooks[event];
+  const entries = Array.isArray(raw) ? raw : isPlainObject(raw) ? [raw] : [];
+  const kept = entries.filter((e) => {
+    if (!e || !Array.isArray(e.hooks)) return true;
+    // Drop entry if ANY of its hooks matches the broken command.
+    return !e.hooks.some(
+      (h) => h && h.type === "command" && h.command === issue.command,
+    );
+  });
+  writeFilteredHooks(settings, settingsPath, event, kept);
+  return {
+    ok: true,
+    message: `Removed broken hook from .claude/settings.json#hooks.${event} (command: ${issue.command})`,
+  };
+}
+
+/**
+ * Registry of stale-artifact handlers. Adding a new kind: append one
+ * entry with a detect function returning issues and a fix function
+ * returning {ok, message}. `handles` lists every issue.kind this entry
+ * accepts (most singular; a pair when one fix covers two kinds).
+ */
+const STALE_DETECTORS = [
+  {
+    detect: detectLegacyHookEvents,
+    fix: fixHookEventEntry,
+    handles: new Set(["legacy-hook-event", "orphan-hook-event"]),
+  },
+  {
+    detect: detectBrokenHookCommands,
+    fix: fixBrokenHookCommand,
+    handles: new Set(["broken-hook-command"]),
+  },
+  {
+    detect: detectLegacyAgileflowPaths,
+    // Split between two fixers based on issue.kind; the runner picks
+    // by handles, so we declare them separately below for clarity.
+    fix: (issue, ctx) =>
+      issue.kind === "legacy-agileflow-file"
+        ? fixFileRemoval(issue, ctx)
+        : fixDirectoryRemoval(issue, ctx),
+    handles: new Set(["legacy-agileflow-subdir", "legacy-agileflow-file"]),
+  },
+  {
+    detect: detectLegacyClaudeSubdirs,
+    fix: fixClaudeSubdirSelective,
+    handles: new Set(["legacy-claude-subdir"]),
+  },
+  {
+    detect: detectBrokenHookScripts,
+    fix: fixBrokenHookScriptStub,
+    handles: new Set(["broken-hook-script"]),
+  },
+  {
+    detect: detectOrphanSkillDirs,
+    fix: fixDirectoryRemoval,
+    handles: new Set(["orphan-skill-dir"]),
+  },
+];
+
+/**
+ * Detect stale AgileFlow artifacts left over from older versions, plugin
+ * renames, or aborted installs. Each issue identifies a path or hook
+ * entry that update wouldn't currently sweep.
+ *
+ * Diagnose-only: never modifies anything. Always returns an array — IO
+ * failures are caught and either yield an issue or are skipped (never
+ * thrown to the caller).
+ *
+ * Issue shape: { severity: "warn"|"error", kind: string, path?: string, message: string }
+ *
+ * @param {string} cwd
+ * @returns {Promise<Array<{severity: string, kind: string, path?: string, message: string}>>}
+ */
+async function checkStaleArtifacts(cwd) {
+  const ctx = buildContext(cwd);
+  const issues = [];
+  for (const entry of STALE_DETECTORS) {
+    issues.push(...(await entry.detect(ctx)));
+  }
+  return issues;
+}
+
+/**
+ * Apply a single stale-artifact fix. Hook-event entries are stripped
+ * from settings.json (preserving user entries in that event); fs
+ * artifacts are removed. Broken hook scripts cannot be auto-fixed —
+ * the script file itself is gone.
+ *
+ * @param {{kind: string, path?: string, message: string}} issue
+ * @param {string} cwd
+ * @returns {{ok: boolean, message: string}}
+ */
+function applyStaleFix(issue, cwd) {
+  const entry = STALE_DETECTORS.find((d) => d.handles.has(issue.kind));
+  if (!entry) {
+    return { ok: false, message: `Unknown issue kind: ${issue.kind}` };
+  }
+  return entry.fix(issue, buildContext(cwd));
+}
+
+/**
+ * `agileflow doctor --fix` body. Detects stale artifacts (same as
+ * `doctor`), then either previews removal (`--fix` alone) or executes
+ * (`--fix --yes`). Returns counts for testing.
+ *
+ * @param {string} cwd
+ * @param {{yes?: boolean, log?: (msg: string) => void}} [opts]
+ * @returns {Promise<{detected: number, fixed: number, failed: number, dryRun: boolean}>}
+ */
+async function doctorFix(cwd, opts = {}) {
+  const log = opts.log || ((m) => console.log(m)); // eslint-disable-line no-console
+  const issues = await checkStaleArtifacts(cwd);
+  if (issues.length === 0) {
+    log("Stale artifacts: ok — nothing to fix.");
+    return { detected: 0, fixed: 0, failed: 0, dryRun: !opts.yes };
+  }
+  if (!opts.yes) {
+    log(
+      `\n${issues.length} stale artifact(s) — dry-run preview (use --yes to actually remove):\n`,
+    );
+    for (const issue of issues) {
+      log(`  • [${issue.kind}] ${issue.message}`);
+      if (issue.path) log(`    ${issue.path}`);
+    }
+    log("\n  Re-run with `agileflow doctor --fix --yes` to apply.");
+    return { detected: issues.length, fixed: 0, failed: 0, dryRun: true };
+  }
+  let fixed = 0;
+  let failed = 0;
+  log(`\nApplying fixes for ${issues.length} stale artifact(s):\n`);
+  for (const issue of issues) {
+    // Guard against synchronous throws from fs.rmSync / unlinkSync on
+    // EPERM/EBUSY/race-deleted paths — otherwise a mid-loop throw
+    // bypasses the final summary log line.
+    try {
+      const r = applyStaleFix(issue, cwd);
+      if (r.ok) {
+        fixed += 1;
+        log(`  ✓ ${r.message}`);
+      } else {
+        failed += 1;
+        log(`  ✗ [${issue.kind}] ${r.message}`);
+      }
+    } catch (err) {
+      failed += 1;
+      log(`  ✗ [${issue.kind}] threw: ${err.message}`);
+    }
+  }
+  log(`\n  ${fixed} fixed, ${failed} skipped/failed.`);
+  return { detected: issues.length, fixed, failed, dryRun: false };
+}
+
+async function doctor(opts = {}) {
+  if (opts && opts.fix) {
+    const cwd = process.cwd();
+    const r = await doctorFix(cwd, { yes: !!opts.yes });
+    if (r.failed > 0) process.exit(1);
+    return;
+  }
   const cwd = process.cwd();
   let totalErrors = 0;
 
   // 1. Plugin manifests (every bundled plugin.yaml).
   const plugins = discoverPlugins();
   const pluginIssues = validatePluginSet(plugins);
-  totalErrors += printSection('Plugin manifests:', pluginIssues);
+  totalErrors += printSection("Plugin manifests:", pluginIssues);
 
   // 2. Skills (every SKILL.md across every bundled plugin).
   const { issues: skillIssues } = await validateBundledSkills();
-  totalErrors += printSection('Skills:', skillIssues);
+  totalErrors += printSection(
+    "Skills:",
+    skillIssues.filter(
+      (i) =>
+        (i.severity !== "warn" && i.severity !== "warning") ||
+        !i.message.includes("_learnings"),
+    ),
+  );
 
   // 3. Aggregated hook manifest (what install would write).
   const aggrErrors = await validateAggregatedHookManifest();
   totalErrors += printSection(
-    'Hook manifest (aggregated):',
-    aggrErrors.map((m) => ({ severity: 'error', message: m })),
+    "Hook manifest (aggregated):",
+    aggrErrors.map((m) => ({ severity: "error", message: m })),
   );
 
   // 4. Installed hook manifest in this cwd (if any).
   const installedErrors = await validateInstalledManifest(cwd);
   totalErrors += printSection(
-    'Hook manifest (installed):',
-    installedErrors.map((m) => ({ severity: 'error', message: m })),
+    "Hook manifest (installed):",
+    installedErrors.map((m) => ({ severity: "error", message: m })),
   );
 
+  // 5. Stale artifacts from older versions / aborted installs.
+  const staleIssues = await checkStaleArtifacts(cwd);
+  // eslint-disable-next-line no-console
+  console.log("\nStale artifacts:");
+  if (staleIssues.length === 0) {
+    // eslint-disable-next-line no-console
+    console.log("  ok");
+  } else {
+    for (const issue of staleIssues) {
+      const label = issue.severity === "error" ? "ERROR" : "WARN ";
+      if (issue.severity === "error") totalErrors += 1;
+      // eslint-disable-next-line no-console
+      console.log(`  ${label} ${issue.message}`);
+      if (issue.path) {
+        // eslint-disable-next-line no-console
+        console.log(`         ${issue.path}`);
+      }
+    }
+    // eslint-disable-next-line no-console
+    console.log(
+      `\n  ${staleIssues.length} stale artifact(s). Run \`agileflow doctor --fix\` to preview removal, or \`--fix --yes\` to apply.`,
+    );
+  }
+
+  // 6. Installation health — skills + hooks in the current project.
+  const installIssues = await checkInstallHealth(cwd);
+  // eslint-disable-next-line no-console
+  console.log("\nInstallation health:");
+  if (installIssues.length === 0) {
+    // eslint-disable-next-line no-console
+    console.log("  ok");
+  } else {
+    for (const issue of installIssues) {
+      if (issue.severity === "info") {
+        // eslint-disable-next-line no-console
+        console.log(`  ✓    ${issue.message}`);
+      } else if (issue.severity === "warn") {
+        // eslint-disable-next-line no-console
+        console.log(`  WARN ${issue.message}`);
+      } else {
+        totalErrors += 1;
+        // eslint-disable-next-line no-console
+        console.log(`  ERROR ${issue.message}`);
+      }
+    }
+  }
+
   // eslint-disable-next-line no-console
-  console.log('');
+  console.log("");
   if (totalErrors === 0) {
     // eslint-disable-next-line no-console
-    console.log('✓ doctor: all checks passed');
+    console.log("✓ doctor: all checks passed");
     return;
   }
   // eslint-disable-next-line no-console
@@ -157,3 +942,6 @@ async function doctor() {
 }
 
 module.exports = doctor;
+module.exports.checkStaleArtifacts = checkStaleArtifacts;
+module.exports.applyStaleFix = applyStaleFix;
+module.exports.doctorFix = doctorFix;