openplanr 3.2.0 → 3.4.0

package/dist/services/runtime-manager/codex-discovery.js

@@ -1,24 +1,11 @@
+import { effectiveCodexHome } from './paths.js';
+export { effectiveCodexHome } from './paths.js';
 import { createHash } from 'node:crypto';
-import { existsSync, lstatSync, readdirSync, readFileSync, realpathSync } from 'node:fs';
+import { existsSync, lstatSync, readdirSync, readFileSync } from 'node:fs';
 import path from 'node:path';
 import { parse } from 'smol-toml';
 import { userHome } from '../../../lib/planr-home.mjs';
 import { inspectRuntimeLocator, inspectRuntimePackage } from './runtime-package.js';
-function canonicalPath(directory) {
-    const resolved = path.resolve(directory);
-    let existing = resolved;
-    while (!existsSync(existing) && path.dirname(existing) !== existing)
-        existing = path.dirname(existing);
-    return path.join(realpathSync(existing), path.relative(existing, resolved));
-}
-/** Uses the native profile selected by the caller, without inspecting other accounts. */
-export function effectiveCodexHome() {
-    const defaultHome = path.resolve(userHome(), '.codex');
-    const selected = process.env.CODEX_HOME?.trim();
-    if (!selected || canonicalPath(selected) === canonicalPath(defaultHome))
-        return defaultHome;
-    return canonicalPath(selected);
-}
 /** Hashes the complete installed closure, including missing or additional support files. */
 function sourceHash(directory) {
     const digest = createHash('sha256');

package/dist/services/runtime-manager/codex-discovery.js.map

@@ -1 +1 @@
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package/dist/services/runtime-manager/doctor.d.ts

@@ -1,3 +1,6 @@
+import { type ClaudeCommandRunner } from '../claude-plugin-service.js';
+import { type CodexCommandRunner } from '../codex-plugin-service.js';
+import { type CodexSkillDiscovery } from './codex-discovery.js';
 import type { OwnedFile } from './global-state.js';
 export type RuntimeDoctorDiagnostic = Readonly<{
     code: string;
@@ -32,4 +35,26 @@ export declare function pluginDocuments(runtime: string, root: string): Installe
  * In a shared file, only the block setup manages is read.
  */
 export declare function diagnoseRetiredCommandSkills(documents: readonly InstalledDocument[], commandRoots: readonly string[], managedBlock: (content: Buffer, marker?: string) => Buffer): RuntimeDoctorDiagnostic | null;
+export declare function runtimeDoctor(projectDir: string, options?: {
+    pipelineRepair?: 'preview' | 'apply';
+    claudeCommandRunner?: ClaudeCommandRunner;
+    codexCommandRunner?: CodexCommandRunner;
+    /** CLI root commands; enables the check for installed skills that still run `planr`. */
+    commandRoots?: readonly string[];
+}): Promise<{
+    ok: boolean;
+    codexDiscovery?: CodexSkillDiscovery;
+    repairs: Array<{
+        id: string;
+        operation: 'remove';
+        target: string;
+        applied: boolean;
+    }>;
+    diagnostics: Array<{
+        code: string;
+        status: 'pass' | 'warn' | 'fail';
+        message: string;
+        fix?: string;
+    }>;
+}>;
 //# sourceMappingURL=doctor.d.ts.map

package/dist/services/runtime-manager/doctor.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../../src/services/runtime-manager/doctor.ts"],"names":[],"mappings":"AASA,OAAO,EACL,KAAK,mBAAmB,EAGzB,MAAM,6BAA6B,CAAC;AACrC,OAAO,EAAE,KAAK,kBAAkB,EAAiC,MAAM,4BAA4B,CAAC;AAGpG,OAAO,EAAE,KAAK,mBAAmB,EAA8B,MAAM,sBAAsB,CAAC;AAE5F,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAC;AAkCnD,MAAM,MAAM,uBAAuB,GAAG,QAAQ,CAAC;IAC7C,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,MAAM,GAAG,MAAM,GAAG,MAAM,CAAC;IACjC,OAAO,EAAE,MAAM,CAAC;IAChB,GAAG,CAAC,EAAE,MAAM,CAAC;CACd,CAAC,CAAC;AAEH,MAAM,MAAM,iBAAiB,GAAG,QAAQ,CAAC;IACvC,OAAO,EAAE,MAAM,CAAC;IAChB,MAAM,EAAE,MAAM,CAAC;IACf,IAAI,CAAC,EAAE,SAAS,CAAC,MAAM,CAAC,CAAC;IACzB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB,CAAC,CAAC;AAQH,wBAAgB,sBAAsB,CAAC,KAAK,EAAE;IAC5C,QAAQ,EAAE,OAAO,CAAC;IAClB,cAAc,EAAE,OAAO,CAAC;IACxB,iBAAiB,EAAE,OAAO,CAAC;CAC5B,GAAG;IACF,KAAK,EAAE,OAAO,CAAC;IACf,YAAY,EAAE,OAAO,CAAC;IACtB,gBAAgB,EAAE,OAAO,CAAC;IAC1B,MAAM,EAAE,MAAM,GAAG,MAAM,GAAG,MAAM,CAAC;CAClC,CAYA;AAED,kFAAkF;AAClF,wBAAgB,2BAA2B,CACzC,KAAK,EAAE,SAAS,SAAS,EAAE,EAC3B,aAAa,EAAE,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,EAAE,IAAI,EAAE,SAAS,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC,EAAE,MAAM,KAAK,MAAM,GAC5F,uBAAuB,GAAG,IAAI,CAwBhC;AAED,qFAAqF;AACrF,wBAAgB,yBAAyB,CAAC,UAAU,EAAE,MAAM,GAAG,uBAAuB,GAAG,IAAI,CA6B5F;AAED,oEAAoE;AACpE,wBAAgB,eAAe,CAAC,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,GAAG,iBAAiB,EAAE,CAKlF;AAED;;;GAGG;AACH,wBAAgB,4BAA4B,CAC1C,SAAS,EAAE,SAAS,iBAAiB,EAAE,EACvC,YAAY,EAAE,SAAS,MAAM,EAAE,EAC/B,YAAY,EAAE,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,KAAK,MAAM,GACzD,uBAAuB,GAAG,IAAI,CA2BhC;AAED,wBAAsB,aAAa,CACjC,UAAU,EAAE,MAAM,EAClB,OAAO,GAAE;IACP,cAAc,CAAC,EAAE,SAAS,GAAG,OAAO,CAAC;IACrC,mBAAmB,CAAC,EAAE,mBAAmB,CAAC;IAC1C,kBAAkB,CAAC,EAAE,kBAAkB,CAAC;IACxC,wFAAwF;IACxF,YAAY,CAAC,EAAE,SAAS,MAAM,EAAE,CAAC;CAC7B,GACL,OAAO,CAAC;IACT,EAAE,EAAE,OAAO,CAAC;IACZ,cAAc,CAAC,EAAE,mBAAmB,CAAC;IACrC,OAAO,EAAE,KAAK,CAAC;QAAE,EAAE,EAAE,MAAM,CAAC;QAAC,SAAS,EAAE,QAAQ,CAAC;QAAC,MAAM,EAAE,MAAM,CAAC;QAAC,OAAO,EAAE,OAAO,CAAA;KAAE,CAAC,CAAC;IACtF,WAAW,EAAE,KAAK,CAAC;QACjB,IAAI,EAAE,MAAM,CAAC;QACb,MAAM,EAAE,MAAM,GAAG,MAAM,GAAG,MAAM,CAAC;QACjC,OAAO,EAAE,MAAM,CAAC;QAChB,GAAG,CAAC,EAAE,MAAM,CAAC;KACd,CAAC,CAAC;CACJ,CAAC,CAuiBD"}

package/dist/services/runtime-manager/doctor.js

@@ -1,6 +1,21 @@
+import { spawnSync } from 'node:child_process';
 import { existsSync, readdirSync, readFileSync } from 'node:fs';
 import path from 'node:path';
+import { CLI_NODE_REMEDIATION, cliNodeVersionMessage, supportsCliNodeVersion, } from '../../../lib/node-runtime.mjs';
 import { CLI_COMMAND, PLANNING_FOLDER } from '../../utils/constants.js';
+import { duplicateClaudePluginDiagnostic, inspectBundledClaudePluginIntegration, } from '../claude-plugin-service.js';
+import { inspectCodexPluginIntegration } from '../codex-plugin-service.js';
+import { resolvePipelinePackage } from '../pipeline-package-service.js';
+import { readOpenPlanrVersion } from '../provenance-service.js';
+import { inspectCodexSkillDiscovery } from './codex-discovery.js';
+import { RuntimeManagerError } from './errors.js';
+import { inferRuntimeScope, loadState, previewHomeProjectCleanup, projectUsesUserRuntime, } from './global-state.js';
+import { runtimeLockManifestDigest, validateRuntimeLockContract, } from './install-plan.js';
+import { detectInstalledRuntimes as detectRuntimes, listInstalledRuntimeAdapters as listRuntimeAdapters, readRegistry, } from './inventory.js';
+import { RETIRED_CLAUDE_AGENT_HASHES, RETIRED_CURSOR_AGENT_RULES, RETIRED_CURSOR_WORKFLOW_RULES, } from './legacy-adapters.js';
+import { codexSkillsRoot, pathIsWithin, planrHome, projectKey, statePath } from './paths.js';
+import { bundledHostRoot, bundledSkillAssets, inspectRuntimeLocator, inspectThinRule, } from './runtime-package.js';
+import { managedBlockBytes, ownershipHash } from './storage.js';
 const SETUP_RUNTIMES = {
     'claude-code': 'claude',
     codex: 'codex',
@@ -118,4 +133,469 @@ export function diagnoseRetiredCommandSkills(documents, commandRoots, managedBlo
             : `Rerun \`${CLI_COMMAND} setup\`, then restart the agent.`,
     };
 }
+export async function runtimeDoctor(projectDir, options = {}) {
+    const diagnostics = [];
+    const repairs = [];
+    let lockedAdapters;
+    const supportedNode = supportsCliNodeVersion(process.versions.node);
+    diagnostics.push({
+        code: 'node-version',
+        status: supportedNode ? 'pass' : 'fail',
+        message: supportedNode
+            ? `Node.js ${process.versions.node}`
+            : cliNodeVersionMessage(process.versions.node),
+        ...(!supportedNode ? { fix: CLI_NODE_REMEDIATION } : {}),
+    });
+    const state = await loadState();
+    const installed = state.projects[projectKey(projectDir)];
+    const detectedRuntimes = detectRuntimes();
+    for (const result of detectedRuntimes) {
+        const configured = installed?.runtimes.includes(result.runtime) ?? false;
+        diagnostics.push({
+            code: `runtime-${result.runtime}`,
+            status: result.installed || !configured ? 'pass' : 'warn',
+            message: result.installed
+                ? `${result.runtime} detected`
+                : configured
+                    ? `${result.runtime} is configured but not detected`
+                    : `${result.runtime} is not installed or configured`,
+            ...(!result.installed && configured
+                ? { fix: `Install ${result.command} only if you intend to use this adapter.` }
+                : {}),
+        });
+    }
+    for (const [runtime, candidates] of [
+        [
+            'claude',
+            Object.keys(RETIRED_CLAUDE_AGENT_HASHES).map((name) => path.join(projectDir, '.claude', 'agents', name)),
+        ],
+        [
+            'cursor',
+            [
+                ...RETIRED_CURSOR_WORKFLOW_RULES.map((name) => path.join(projectDir, '.cursor', 'rules', name)),
+                ...RETIRED_CURSOR_AGENT_RULES.map((name) => path.join(projectDir, '.cursor', 'rules', 'agents', name)),
+            ],
+        ],
+    ]) {
+        const leftovers = candidates.filter((target) => existsSync(target));
+        if (leftovers.length === 0)
+            continue;
+        diagnostics.push({
+            code: `runtime-${runtime}-legacy-agents`,
+            status: 'warn',
+            message: `Potential legacy ${runtime} adapter paths remain: ${leftovers.join(', ')}`,
+            fix: `Run \`${CLI_COMMAND} setup --runtime ${runtime} --scope project --dry-run\`, then rerun without --dry-run to back up and retire recognized generated files. Modified or unknown files are preserved; review those manually.`,
+        });
+    }
+    const pipeline = resolvePipelinePackage(false);
+    diagnostics.push({
+        code: 'pipeline-package',
+        status: pipeline ? 'pass' : 'warn',
+        message: pipeline
+            ? `Optional deterministic pipeline utilities ${pipeline.version}`
+            : 'Optional deterministic pipeline utilities are not installed',
+        ...(!pipeline
+            ? { fix: 'Install optional dependencies only if you need pipeline utilities.' }
+            : {}),
+    });
+    const registry = listRuntimeAdapters();
+    for (const adapter of registry) {
+        const detected = detectedRuntimes.find((entry) => entry.runtime === adapter.id)?.installed;
+        const configured = installed?.runtimes.includes(adapter.id) ?? false;
+        if (!detected && !configured)
+            continue;
+        const mode = adapter.capabilities?.interactiveQuestions;
+        diagnostics.push({
+            code: `runtime-interaction-${adapter.id}`,
+            status: mode ? 'pass' : 'fail',
+            message: mode
+                ? `${adapter.id} uses ${mode} host-native questions`
+                : `${adapter.id} does not declare a host-native question capability`,
+            ...(!mode ? { fix: 'Reinstall the OpenPlanr utility CLI host package.' } : {}),
+        });
+    }
+    try {
+        const counts = {
+            claude: new Set(bundledSkillAssets('claude-code').map(({ skillId }) => skillId)).size,
+            codex: new Set(bundledSkillAssets('codex').map(({ skillId }) => skillId)).size,
+            cursor: new Set(bundledSkillAssets('cursor').map(({ skillId }) => skillId)).size,
+        };
+        const uniqueCounts = new Set(Object.values(counts));
+        const current = uniqueCounts.size === 1 && counts.claude > 0;
+        diagnostics.push({
+            code: 'host-skill-packages',
+            status: current ? 'pass' : 'fail',
+            message: current
+                ? `Claude Code, Codex, and Cursor each expose all ${counts.claude} host-native skills`
+                : `Host skill package membership drifted (${JSON.stringify(counts)})`,
+            ...(!current ? { fix: 'Reinstall the CLI or regenerate its host packages.' } : {}),
+        });
+    }
+    catch (cause) {
+        diagnostics.push({
+            code: 'host-skill-packages',
+            status: 'fail',
+            message: cause instanceof Error ? cause.message : String(cause),
+            fix: 'Reinstall the CLI or regenerate its host packages.',
+        });
+    }
+    const claudeManagedAtUserScope = Object.values(state.projects).some((project) => project.runtimes.includes('claude-code') &&
+        ['user', 'both'].includes(project.runtimeScopes?.['claude-code'] ??
+            inferRuntimeScope(project.ownedFiles, 'claude-code')));
+    const pluginSkillDocuments = [];
+    const claudeDetected = Boolean(options.claudeCommandRunner) ||
+        (detectedRuntimes.find((runtime) => runtime.runtime === 'claude-code')?.installed ?? false);
+    if (claudeDetected && claudeManagedAtUserScope) {
+        const inspection = inspectBundledClaudePluginIntegration(bundledHostRoot('claude'), options.claudeCommandRunner);
+        if (inspection.error) {
+            diagnostics.push({
+                code: 'runtime-claude-plugins',
+                status: 'fail',
+                message: `Claude plugin state could not be inspected: ${inspection.error}`,
+                fix: `Update Claude Code, then run \`${CLI_COMMAND} runtime update claude --scope user\`.`,
+            });
+        }
+        else {
+            for (const root of [
+                ...inspection.plugins.flatMap((plugin) => plugin.installPath ?? []),
+                ...inspection.duplicatePluginPaths,
+            ]) {
+                pluginSkillDocuments.push(...pluginDocuments('claude-code', root));
+            }
+            const drift = inspection.plugins.filter((plugin) => !plugin.installed ||
+                !plugin.enabled ||
+                !plugin.identityValid ||
+                plugin.installedVersion !== plugin.expectedVersion);
+            diagnostics.push({
+                code: 'runtime-claude-plugins',
+                status: inspection.ready ? 'pass' : 'fail',
+                message: inspection.ready
+                    ? `Claude plugins match compatibility versions (${inspection.plugins
+                        .map((plugin) => `${plugin.name} ${plugin.expectedVersion}`)
+                        .join(', ')})`
+                    : `Claude plugin drift detected: ${drift
+                        .map((plugin) => `${plugin.id} ${plugin.installedVersion ?? 'missing'} → ${plugin.expectedVersion}${!plugin.identityValid ? ' (invalid identity)' : ''}`)
+                        .join(', ')}`,
+                ...(!inspection.ready
+                    ? {
+                        fix: `Run \`${CLI_COMMAND} runtime update claude --scope user\` and restart Claude Code.`,
+                    }
+                    : {}),
+            });
+            if (inspection.staleMarketplacePath) {
+                diagnostics.push({
+                    code: 'runtime-claude-marketplace-path',
+                    status: 'fail',
+                    message: `The local OpenPlanr Claude marketplace points to another install: ${inspection.staleMarketplacePath}, not ${bundledHostRoot('claude')}`,
+                    fix: `Run \`${CLI_COMMAND} setup --runtime claude --scope user\` to point it at this install.`,
+                });
+            }
+            if (inspection.legacyPluginIds.length > 0) {
+                diagnostics.push({
+                    code: 'runtime-claude-legacy-plugin',
+                    status: 'warn',
+                    message: `Legacy Claude plugin installation detected: ${inspection.legacyPluginIds.join(', ')}`,
+                    fix: 'Verify `planr@openplanr-local`, then remove the legacy plugin from Claude Code.',
+                });
+            }
+            if (inspection.duplicatePluginIds.length > 0) {
+                diagnostics.push({
+                    code: 'runtime-claude-duplicate-plugin',
+                    status: 'warn',
+                    ...duplicateClaudePluginDiagnostic(inspection),
+                });
+            }
+        }
+    }
+    const expectsProjectLock = installed?.ownedFiles.some((file) => file.scope === 'project') ?? false;
+    const lock = path.join(projectDir, PLANNING_FOLDER, 'runtime-lock.json');
+    if (!existsSync(lock)) {
+        // User-scope setup is recorded under the directory it ran in but serves every project.
+        const managed = Boolean(installed) ||
+            Object.values(state.projects).some((project) => project.runtimes.some((runtime) => projectUsesUserRuntime(project, runtime)));
+        const lockStatus = expectsProjectLock ? 'warn' : managed ? 'pass' : 'warn';
+        diagnostics.push({
+            code: 'runtime-lock',
+            status: lockStatus,
+            message: expectsProjectLock
+                ? 'Project runtime lock missing'
+                : managed
+                    ? 'User-scope setup does not require a project runtime lock'
+                    : 'No managed runtime setup found for this directory',
+            ...(expectsProjectLock
+                ? { fix: `Run \`${CLI_COMMAND} setup --scope project\`.` }
+                : !managed
+                    ? { fix: `Run \`${CLI_COMMAND} setup\`.` }
+                    : {}),
+        });
+    }
+    else {
+        try {
+            const value = JSON.parse(readFileSync(lock, 'utf8'));
+            const errors = validateRuntimeLockContract(value);
+            if (errors.length) {
+                throw new RuntimeManagerError('E_RUNTIME_LOCK_INVALID', 'Project runtime lock does not match the supported contract.');
+            }
+            lockedAdapters = value.adapters;
+            const cliVersion = readOpenPlanrVersion();
+            const cliDrift = value.components?.cli !== cliVersion;
+            const componentDrift = cliDrift ||
+                (pipeline && value.components?.pipeline !== pipeline.version) ||
+                value.components?.skills !== readRegistry().pluginVersion;
+            const expectedDigest = runtimeLockManifestDigest({
+                protocolVersion: value.protocolVersion,
+                pipelineVersion: value.components?.pipeline,
+                adapters: value.adapters,
+                skillModes: value.skillModes,
+            });
+            const digestDrift = value.manifestDigest !== expectedDigest;
+            const registry = listRuntimeAdapters();
+            const adapterDrift = (value.adapters ?? []).some((locked) => {
+                const current = registry.find((adapter) => adapter.id === locked.runtime);
+                return (!current ||
+                    current.version !== locked.version ||
+                    current.capabilityLevel !== locked.capabilityLevel);
+            });
+            // An OpenPlanr upgrade advances the CLI version the lock recorded.
+            // When the CLI component trails the installed build and nothing that
+            // governs runtime dispatch (runtime adapters, manifest digest)
+            // diverged, the lock is simply behind an expected upgrade — surface it as
+            // an informational `warn`, not a `fail` implying the board is broken. A
+            // digest/adapter drift, or a component drift that does not include the CLI
+            // (for example a pinned obsolete skill bundle), remains a genuine `fail`.
+            // The warn/fail derivation lives in the single `classifyComponentDrift`
+            // helper so `openplanr upgrade status` reuses this exact distinction rather
+            // than re-deriving it; a digest/adapter drift is doctor's
+            // flavour of an incompatible tuple.
+            const { drift, genuineDrift, upgradeOnlyDrift, status } = classifyComponentDrift({
+                cliDrift,
+                componentDrift: Boolean(componentDrift),
+                incompatibleDrift: digestDrift || adapterDrift,
+            });
+            diagnostics.push({
+                code: drift ? 'lock-drift' : 'runtime-lock',
+                status,
+                message: genuineDrift
+                    ? `Runtime lock drift detected (components: ${componentDrift}, digest: ${digestDrift}, adapters: ${adapterDrift})`
+                    : upgradeOnlyDrift
+                        ? `Runtime lock component versions trail an OpenPlanr upgrade (components: ${componentDrift}); this is expected after upgrading and does not affect runtime execution`
+                        : drift
+                            ? `Runtime lock drift detected (components: ${componentDrift}, digest: ${digestDrift}, adapters: ${adapterDrift})`
+                            : 'Project runtime lock matches installed component versions',
+                ...(drift
+                    ? {
+                        fix: upgradeOnlyDrift
+                            ? `Run \`${CLI_COMMAND} runtime update all --scope project\` to refresh the lock to the upgraded component versions.`
+                            : `Run \`${CLI_COMMAND} runtime update all --scope project\`.`,
+                    }
+                    : {}),
+            });
+        }
+        catch {
+            diagnostics.push({
+                code: 'runtime-lock-invalid',
+                status: 'fail',
+                message: 'Project runtime lock is not valid JSON or does not match the supported contract',
+                fix: `Run \`${CLI_COMMAND} setup --scope project\` after reviewing the existing lock.`,
+            });
+        }
+    }
+    if (installed) {
+        if (lockedAdapters) {
+            const lockedState = lockedAdapters
+                .map((adapter) => `${adapter.runtime}:${adapter.installScope}`)
+                .sort();
+            const installedState = installed.runtimes
+                .map((runtime) => `${runtime}:${installed.runtimeScopes?.[runtime] ?? inferRuntimeScope(installed.ownedFiles, runtime)}`)
+                .sort();
+            const stateDrift = JSON.stringify(lockedState) !== JSON.stringify(installedState);
+            diagnostics.push({
+                code: stateDrift ? 'lock-state-drift' : 'lock-state',
+                status: stateDrift ? 'fail' : 'pass',
+                message: stateDrift
+                    ? 'Runtime lock adapters do not match the managed installation state'
+                    : 'Runtime lock adapters match the managed installation state',
+                ...(stateDrift
+                    ? { fix: `Run \`${CLI_COMMAND} setup --dry-run\`, then approve the repair.` }
+                    : {}),
+            });
+        }
+    }
+    else if (lockedAdapters?.length) {
+        diagnostics.push({
+            code: 'runtime-state-missing',
+            status: 'warn',
+            message: 'The project has a runtime lock but this machine has no managed adapter state',
+            fix: `Run \`${CLI_COMMAND} setup\` to install the locked runtime adapters on this machine.`,
+        });
+    }
+    const globallyOwned = Object.values(state.userBundles ?? {}).flatMap((bundle) => bundle?.ownedFiles ?? []);
+    const managedFiles = [
+        ...(installed?.ownedFiles ?? []),
+        ...globallyOwned.filter((file, index, files) => files.findIndex((candidate) => candidate.target === file.target) === index),
+    ];
+    const managedFileDiagnostic = diagnoseManagedRuntimeFiles(managedFiles, ownershipHash);
+    if (managedFileDiagnostic)
+        diagnostics.push(managedFileDiagnostic);
+    const commandDiagnostic = diagnoseRetiredCommandSkills([...managedFiles, ...pluginSkillDocuments], options.commandRoots ?? [], managedBlockBytes);
+    if (commandDiagnostic)
+        diagnostics.push(commandDiagnostic);
+    const verifiedPackages = new Map();
+    const closureFailures = [];
+    for (const file of managedFiles) {
+        try {
+            if (path.basename(file.target) === 'openplanr.install.json')
+                inspectRuntimeLocator(path.dirname(file.target), verifiedPackages);
+            else if (file.runtime === 'cursor' && file.target.endsWith('.mdc'))
+                inspectThinRule(file.target, verifiedPackages);
+        }
+        catch (cause) {
+            closureFailures.push(`${file.target}: ${cause instanceof Error ? cause.message : String(cause)}`);
+        }
+    }
+    if (verifiedPackages.size || closureFailures.length)
+        diagnostics.push({
+            code: 'runtime-package-custody',
+            status: closureFailures.length ? 'fail' : 'pass',
+            message: closureFailures.length
+                ? `Pinned runtime package verification failed: ${closureFailures.join('; ')}`
+                : 'Pinned runtime packages match their complete content inventories',
+            ...(closureFailures.length
+                ? {
+                    fix: `Run \`${CLI_COMMAND} doctor --fix\` to preview the repair; changed package files are backed up before anything is replaced.`,
+                }
+                : {}),
+        });
+    let codexDiscovery;
+    const codexBundle = state.userBundles?.codex;
+    if (options.codexCommandRunner ||
+        detectedRuntimes.some((runtime) => runtime.runtime === 'codex' && runtime.installed)) {
+        const configuredMode = codexBundle?.installMode ?? installed?.skillModes?.codex ?? 'direct';
+        const inspection = inspectCodexPluginIntegration(bundledHostRoot('openai'), configuredMode, configuredMode, options.codexCommandRunner);
+        codexDiscovery = inspectCodexSkillDiscovery({
+            hostPackageRoot: bundledHostRoot('openai'),
+            projectDir,
+            mode: configuredMode,
+            packageVersion: readOpenPlanrVersion(),
+            ownershipStatePath: statePath(),
+            activePlugin: inspection.installed
+                ? { id: inspection.pluginId, version: inspection.installedVersion }
+                : undefined,
+        });
+        diagnostics.push({
+            code: 'runtime-codex-profile',
+            status: 'pass',
+            message: `Effective Codex profile: ${codexDiscovery.effectiveHome}; ownership: ${statePath()}`,
+        });
+        const stale = codexDiscovery.skills.filter((skill) => skill.resolution === 'stale');
+        const ambiguous = codexDiscovery.skills.filter((skill) => skill.resolution === 'ambiguous');
+        const missing = codexDiscovery.skills.filter((skill) => skill.resolution === 'missing');
+        const unreadable = codexDiscovery.skills.filter((skill) => skill.resolution === 'unreadable');
+        const oldCaches = codexDiscovery.skills.filter((skill) => skill.copies.some((copy) => copy.kind === 'plugin-cache' && !copy.current && copy.enabled !== true));
+        if (stale.length ||
+            ambiguous.length ||
+            missing.length ||
+            unreadable.length ||
+            codexDiscovery.issues.length) {
+            diagnostics.push({
+                code: 'runtime-codex-skill-resolution',
+                status: 'warn',
+                message: `${stale.length} stale skill(s), ${missing.length} missing skill(s), ${unreadable.length} unreadable skill(s), ${ambiguous.length} multiple discovery path(s), ${oldCaches.length} skill(s) with inactive cached copies. CLI package ${codexDiscovery.packageVersion}; per-skill and Protocol versions, paths and closure hashes are in doctor --json. An already-open session may retain earlier skills.`,
+                fix: `Run \`${CLI_COMMAND} setup --runtime codex --dry-run\` in this profile, review the installer repair, then restart Codex. Do not delete plugin caches by hand.`,
+            });
+        }
+        if (oldCaches.length > 0) {
+            diagnostics.push({
+                code: 'runtime-codex-cache-history',
+                status: 'pass',
+                message: `${oldCaches.length} skill(s) have inactive cached copies. These do not imply enabled duplicates; restart Codex if an open session still shows earlier skills.`,
+            });
+        }
+        const directSkillFiles = codexBundle?.ownedFiles.filter((file) => pathIsWithin(file.target, codexSkillsRoot()))
+            .length ?? 0;
+        if (inspection.error) {
+            diagnostics.push({
+                code: 'runtime-codex-plugin',
+                status: 'warn',
+                message: `Codex plugin state could not be inspected: ${inspection.error}`,
+                fix: `Run \`${CLI_COMMAND} setup --runtime codex --dry-run\` for an exact repair preview.`,
+            });
+        }
+        else {
+            diagnostics.push({
+                code: 'runtime-codex-install-mode',
+                status: inspection.ready ? 'pass' : 'warn',
+                message: inspection.ready
+                    ? `Codex ${configuredMode} discovery is current`
+                    : inspection.operations.length > 0
+                        ? `Codex ${configuredMode} discovery needs repair: ${inspection.operations.map((operation) => operation.description).join('; ')}`
+                        : `Codex ${configuredMode} discovery has conflicting enabled registrations: ${inspection.duplicates.join(', ')}`,
+                ...(inspection.ready
+                    ? {}
+                    : {
+                        fix: `Run \`${CLI_COMMAND} doctor --fix\` to preview repairs while preserving your saved discovery choice.`,
+                    }),
+            });
+            if ((directSkillFiles > 0 && inspection.installed) || inspection.duplicates.length > 0) {
+                diagnostics.push({
+                    code: 'runtime-codex-duplicate-discovery',
+                    status: 'warn',
+                    message: `Codex has duplicate OpenPlanr discovery ownership${inspection.duplicates.length ? `: ${inspection.duplicates.join(', ')}` : ' across direct skills and the unified plugin'}`,
+                    fix: 'Choose direct or unified-plugin mode, preview setup, and use --replace-managed only for manifest-owned content.',
+                });
+            }
+        }
+    }
+    const accidentalHomeFiles = await previewHomeProjectCleanup();
+    if (accidentalHomeFiles.length > 0) {
+        diagnostics.push({
+            code: 'home-project-install',
+            status: 'warn',
+            message: `${accidentalHomeFiles.length} project-scoped managed file(s) were installed in the home directory`,
+            fix: `Run \`${CLI_COMMAND} doctor --fix\` to preview and remove only recorded OpenPlanr-owned project content.`,
+        });
+    }
+    const provenanceDiagnostic = diagnoseRuntimeProvenance(projectDir);
+    if (provenanceDiagnostic)
+        diagnostics.push(provenanceDiagnostic);
+    if (pipeline) {
+        // The child gets the resolved home only, so it does not repeat the OPENPLANR_HOME warning.
+        const { OPENPLANR_HOME: _deprecatedHome, ...inheritedEnvironment } = process.env;
+        const result = spawnSync(process.execPath, [
+            path.join(pipeline.root, 'scripts', 'doctor.mjs'),
+            '--json',
+            ...(options.pipelineRepair === 'preview' ? ['--repair-preview'] : []),
+            ...(options.pipelineRepair === 'apply' ? ['--fix'] : []),
+        ], {
+            cwd: projectDir,
+            encoding: 'utf8',
+            windowsHide: true,
+            env: { ...inheritedEnvironment, PLANR_HOME: planrHome() },
+        });
+        try {
+            const report = JSON.parse(result.stdout);
+            repairs.push(...(report.repairs ?? []));
+            for (const check of report.checks ?? []) {
+                if (check.status === 'ok')
+                    continue;
+                diagnostics.push({
+                    code: `pipeline-${check.id}`,
+                    status: check.status,
+                    message: check.message,
+                    ...(check.fix ? { fix: check.fix } : {}),
+                });
+            }
+        }
+        catch {
+            diagnostics.push({
+                code: 'pipeline-doctor-unavailable',
+                status: 'warn',
+                message: 'The pipeline doctor did not return valid JSON',
+                fix: `Run \`${CLI_COMMAND} doctor\` for direct diagnostics.`,
+            });
+        }
+    }
+    const fail = diagnostics.some((item) => item.status === 'fail');
+    return { ok: !fail, diagnostics, repairs, ...(codexDiscovery ? { codexDiscovery } : {}) };
+}
 //# sourceMappingURL=doctor.js.map