@technomoron/agent-run 0.99.21 → 0.99.23

package/dist/agent-run.js

@@ -7,23 +7,35 @@ exports.resolveAgentDir = resolveAgentDir;
 exports.findProjectRoot = findProjectRoot;
 exports.resolveProfile = resolveProfile;
 exports.defaultConfigRoot = defaultConfigRoot;
+exports.defaultConfigRootSearchCandidates = defaultConfigRootSearchCandidates;
+exports.parseEditorCommand = parseEditorCommand;
 const childProcess = require("child_process");
 const fs = require("fs");
 const os = require("os");
 const path = require("path");
+const crossSpawn = require("cross-spawn");
 const jsonc_parser_1 = require("jsonc-parser");
 const nunjucks = require("nunjucks");
 const IS_WINDOWS = process.platform === 'win32';
 const ENV_FILE_NAME = '.agent-run.env';
 const IGNORE_FILE_NAME = '.agent-run-ignore';
-const LOCAL_AI_FILE_NAMES = new Set(['AGENTS.md', 'AGENTS-MODS.md', 'AGENTS.override.md', 'CLAUDE.md', 'codex.md']);
+const LOCAL_AI_FILE_NAMES = new Set([
+    'AGENTS.md',
+    'AGENTS-MODS.md',
+    'AGENTS.override.md',
+    'CLAUDE.md',
+    'CLAUDE.local.md',
+    '.mcp.json',
+    'codex.md'
+]);
+const LOCAL_AI_DIRECTORY_NAMES = new Set(['.agents', '.claude', '.codex']);
 const CONFIG_ROOT_OVERRIDE_ENV = 'AGENT_RUN_CONFIG_ROOT_OVERRIDE';
 const CONFIG_DIR_ENV = 'AGENT_CONFIG_DIR';
 const VERBOSE_ENV = 'AGENT_RUN_VERBOSE';
 const MANIFEST_FILE_NAME = 'agent-run.jsonc';
 const LOCAL_TEMPLATE_FILE_NAME = 'local.md.njk';
 const LIVE_DIR_NAME = 'live';
-const PACKAGE_VERSION = '0.99.16';
+const PACKAGE_VERSION = '0.99.23';
 const UNEXPANDED_TEMPLATE_RE = /\{\{[^}]+\}\}|\{%[^%]+%\}/;
 const agentRunEnvCache = new Map();
 const GENERATED_GITIGNORE_ENTRIES = [
@@ -31,7 +43,24 @@ const GENERATED_GITIGNORE_ENTRIES = [
     '**/live/',
     '',
     '# Optional generated caches',
-    '**/.agent-run-cache/'
+    '**/.agent-run-cache/',
+    '',
+    '# Legacy Codex runtime state',
+    '**/auth.json',
+    '**/history.jsonl',
+    '**/sessions/',
+    '**/archived_sessions/',
+    '**/log/',
+    '**/logs/',
+    '**/shell_snapshots/',
+    '**/*.sqlite*',
+    '**/models_cache.json',
+    '**/cache/',
+    '**/.tmp/',
+    '**/installation_id',
+    '**/version.json',
+    '**/.personality_migration',
+    '**/skills/.system/'
 ];
 const REQUIRED_GLOBAL_TEMPLATES = [
     'global/agents/code.md.njk',
@@ -217,6 +246,7 @@ function parseRunCommand(command, inputArgs) {
         }
         if (arg === '--') {
             passthrough = true;
+            args.push(arg);
             continue;
         }
         if (arg === '--none') {
@@ -261,15 +291,15 @@ function parseRunCommand(command, inputArgs) {
         }
         if (arg === '--network') {
             if (command !== 'codex') {
-                fail('--network is only supported for agent-run codex --sandboxed');
+                fail('--network is only supported for agent-run codex');
             }
             wrapperArgs.codexNetwork = true;
             continue;
         }
         args.push(arg);
     }
-    if (wrapperArgs.codexNetwork && wrapperArgs.codexSandboxMode !== 'sandboxed') {
-        fail('--network is only meaningful with agent-run codex --sandboxed');
+    if (wrapperArgs.codexNetwork && wrapperArgs.codexSandboxMode === 'danger') {
+        fail('--network cannot be combined with agent-run codex --danger');
     }
     return { args, command, wrapperArgs };
 }
@@ -442,9 +472,9 @@ function renderHelp(topic) {
                 '  --generate         Generate files without running the tool',
                 '',
                 'Codex wrapper options:',
-                '  --danger           Run Codex with no sandbox: -a never -s danger-full-access (default)',
-                '  --sandboxed        Run Codex with workspace-write sandbox',
-                '  --network          Enable network for --sandboxed via config override',
+                '  --danger           Run Codex with no sandbox: -a never -s danger-full-access',
+                '  --sandboxed        Run Codex with workspace-write sandbox (default)',
+                '  --network          Enable network for the workspace-write sandbox',
                 ''
             ].join('\n');
     }
@@ -524,23 +554,29 @@ function runTool(parsed) {
         fail(profileResult.reason);
     }
     const profile = profileResult.profile;
-    const configRoot = defaultConfigRoot(projectRoot);
-    const agentDir = resolveAgentDir(projectRoot);
     if (wrapperArgs.show) {
+        const configRoot = defaultConfigRoot(projectRoot);
+        const agentDir = path.join(configRoot, profile);
+        verbose(`profile=${profile} configRoot=${configRoot} agentPath=${agentDir}`);
         showToolProfile(command, projectRoot, agentDir);
         return;
     }
     if (wrapperArgs.create) {
         runInit({ command: 'init', targetPath: projectRoot });
     }
+    const configRoot = defaultConfigRoot(projectRoot);
+    const agentDir = path.join(configRoot, profile);
+    verbose(`profile=${profile} configRoot=${configRoot} agentPath=${agentDir}`);
     ensureRunnableProfile(configRoot, agentDir, profile);
+    const preview = renderProfile(projectRoot, agentDir, true, command);
+    ensureToolEnabled(preview.context, command);
     if (wrapperArgs.generate) {
         const rendered = syncAgentProfile(projectRoot, agentDir);
         printUpdateSummary(rendered);
         return;
     }
     const localAiFiles = findLocalAiFiles(projectRoot, agentDir);
-    if (localAiFiles.length > 0) {
+    if (preview.context.guardrails.forbidRepoAiFiles && localAiFiles.length > 0) {
         if (!wrapperArgs.local) {
             failForLocalAiFiles(command, projectRoot, localAiFiles);
         }
@@ -548,16 +584,17 @@ function runTool(parsed) {
     }
     const realBinary = findRealBinary(command);
     const permissionArgs = getPermissionArgs(command);
-    syncAgentProfile(projectRoot, agentDir);
+    const rendered = syncAgentProfile(projectRoot, agentDir);
     if (command === 'codex') {
-        runCodex(realBinary, permissionArgs, agentDir, configRoot, args, projectRoot, wrapperArgs);
+        runCodex(realBinary, permissionArgs, rendered.context, args, wrapperArgs);
         return;
     }
-    runClaude(realBinary, permissionArgs, agentDir, configRoot, args, projectRoot, wrapperArgs);
+    runClaude(realBinary, permissionArgs, rendered.context, args, wrapperArgs);
 }
 function showToolProfile(command, projectRoot, agentDir) {
     const trace = { sourceFiles: new Set() };
     const rendered = renderProfile(projectRoot, agentDir, true, command, trace);
+    ensureToolEnabled(rendered.context, command);
     const generatedFiles = uniqueSorted(rendered.files.map((file) => file.path));
     const sourceFiles = uniqueSorted([...trace.sourceFiles]);
     process.stdout.write([
@@ -574,6 +611,11 @@ function showToolProfile(command, projectRoot, agentDir) {
         ''
     ].join('\n'));
 }
+function ensureToolEnabled(context, command) {
+    if (!context.tools[command]) {
+        fail(`${command} is disabled for agent-run profile ${context.profile}`);
+    }
+}
 function uniqueSorted(values) {
     return [...new Set(values.map((value) => path.resolve(value)))].sort((a, b) => a.localeCompare(b));
 }
@@ -588,8 +630,9 @@ function runInit(parsed) {
         return;
     }
     const profile = resolveProfile(projectRoot);
-    const configRoot = defaultConfigRoot(projectRoot);
-    const agentDir = resolveAgentDir(projectRoot);
+    const configRoot = defaultConfigRoot(projectRoot, { preferProjectRoot: true });
+    const agentDir = path.join(configRoot, profile);
+    verbose(`profile=${profile} configRoot=${configRoot} agentPath=${agentDir}`);
     ensureConfigRootLayout(configRoot);
     ensureConfigRootGitignore(configRoot);
     ensureDefaultGlobalTemplates(configRoot);
@@ -895,31 +938,20 @@ function convertLegacyTemplateVars(content) {
         .replace(/^\n{2,}/, '\n');
 }
 function migrateCodexRuntimeFiles(agentDir) {
-    const runtimeNames = [
-        '.personality_migration',
-        '.tmp',
-        'auth.json',
-        'cache',
-        'history.jsonl',
-        'installation_id',
-        'log',
-        'logs_2.sqlite',
-        'models_cache.json',
-        'sessions',
-        'shell_snapshots',
-        'skills',
-        'state_5.sqlite',
-        'tmp',
-        'version.json'
-    ];
-    const codexHome = path.join(agentDir, 'memories', 'codex-home');
+    const runtimeNames = fs
+        .readdirSync(agentDir)
+        .filter((name) => /^(?:\.personality_migration|\.tmp|auth\.json|cache|history\.jsonl|installation_id|log|logs|models_cache\.json|sessions|archived_sessions|shell_snapshots|skills|tmp|version\.json)$/.test(name) || /^(?:logs|state)_.*\.sqlite(?:-.+)?$/.test(name));
+    const codexHome = path.join(agentDir, LIVE_DIR_NAME, 'memories', 'codex-home');
     let moved = 0;
     for (const name of runtimeNames) {
         const source = path.join(agentDir, name);
-        const target = path.join(codexHome, name);
-        if (!fs.existsSync(source) || fs.existsSync(target)) {
+        if (!fs.existsSync(source) && !isSymlink(source)) {
             continue;
         }
+        let target = path.join(codexHome, name);
+        if (fs.existsSync(target) || isSymlink(target)) {
+            target = nextBackupPath(target);
+        }
         fs.mkdirSync(path.dirname(target), { recursive: true });
         fs.renameSync(source, target);
         moved += 1;
@@ -1081,7 +1113,11 @@ function normalizeManifest(manifest, profile) {
     };
 }
 function normalizeSkillName(name) {
-    return name === 'code-review' ? 'code-review-organizer' : name;
+    const normalized = name === 'code-review' ? 'code-review-organizer' : name;
+    if (!/^[A-Za-z0-9._-]+$/.test(normalized)) {
+        throw new Error(`invalid skill name: ${name}`);
+    }
+    return normalized;
 }
 function normalizeInstalledSkills(names) {
     return [...new Set(names.map(normalizeSkillName))];
@@ -1108,12 +1144,13 @@ function defaultAgentIncludesForProfile(profile) {
     return [`{{ profile }}/${LOCAL_TEMPLATE_FILE_NAME}`, `{{ profile }}/AGENTS-MODS.md`];
 }
 function createNunjucksEnv(configRoot) {
-    return new nunjucks.Environment(new nunjucks.FileSystemLoader(configRoot, { noCache: true }), {
+    const env = new nunjucks.Environment(new nunjucks.FileSystemLoader(configRoot, { noCache: true }), {
         autoescape: false,
         trimBlocks: true,
         lstripBlocks: true,
         throwOnUndefined: true
     });
+    return env;
 }
 function buildRenderContext(projectRoot, profileDir, configRoot, manifest, env) {
     const date = localDateString();
@@ -1127,6 +1164,7 @@ function buildRenderContext(projectRoot, profileDir, configRoot, manifest, env)
         configRoot,
         date,
         checks: manifest.checks,
+        tools: manifest.tools,
         guardrails: manifest.guardrails
     };
     const reviewDir = resolveRuntimePath(configRoot, manifest.paths.reviewDir, env, baseContext);
@@ -1295,20 +1333,23 @@ function renderProfile(projectRoot, agentDir, checkOnly = false, targetTool = nu
     });
     context.skills = renderSkills(env, configRoot, manifest, context, trace);
     const files = [];
-    if (targetTool === null || targetTool === 'codex') {
+    if (context.tools.codex && (targetTool === null || targetTool === 'codex')) {
         const agentsContent = renderToolInstructions('AGENTS.md', env, configRoot, context, false, trace);
-        files.push({ path: path.join(context.paths.liveDir, 'AGENTS.md'), content: agentsContent });
-        files.push({ path: path.join(context.paths.liveDir, 'config.toml'), content: renderCodexConfig(env, configRoot, context, trace) });
+        files.push({ path: path.join(context.paths.codexHomeDir, 'AGENTS.md'), content: agentsContent });
+        files.push({ path: path.join(context.paths.codexHomeDir, 'config.toml'), content: renderCodexConfig(env, configRoot, context, trace) });
         files.push(...renderNativeSkillFiles(context, 'codex'));
     }
-    if (targetTool === null || targetTool === 'claude') {
+    if (context.tools.claude && (targetTool === null || targetTool === 'claude')) {
         const claudeContent = renderToolInstructions('CLAUDE.md', env, configRoot, context, true, trace);
         files.push({ path: path.join(context.paths.liveDir, 'CLAUDE.md'), content: claudeContent });
-        files.push({ path: path.join(context.paths.liveDir, '.claude', 'CLAUDE.md'), content: claudeContent });
         files.push({
             path: path.join(context.paths.liveDir, '.claude', 'agent-run-settings.json'),
             content: renderClaudeSettings(env, configRoot, context, trace)
         });
+        files.push({
+            path: path.join(context.paths.liveDir, '.claude', '.claude-plugin', 'plugin.json'),
+            content: claudePluginManifestContent(context)
+        });
         files.push(...renderNativeSkillFiles(context, 'claude'));
     }
     files.push(...renderGuardShims(context));
@@ -1324,12 +1365,61 @@ function renderProfile(projectRoot, agentDir, checkOnly = false, targetTool = nu
 function syncAgentProfile(projectRoot, agentDir, options) {
     const rendered = renderProfile(projectRoot, agentDir, false, null, undefined, options);
     syncRuntimeDirs(rendered.context);
+    removeStaleGeneratedEntries(rendered);
     for (const file of rendered.files) {
         writeGeneratedFile(file.path, file.content, file.executable ?? false);
     }
+    removeLegacyGeneratedCodexFiles(rendered.context);
     removeLegacyGeneratedClaudeSettings(rendered.context);
     return rendered;
 }
+function removeStaleGeneratedEntries(rendered) {
+    const expectedFiles = new Set(rendered.files.map((file) => path.resolve(file.path)));
+    for (const filePath of [
+        path.join(rendered.context.paths.codexHomeDir, 'AGENTS.md'),
+        path.join(rendered.context.paths.codexHomeDir, 'config.toml'),
+        path.join(rendered.context.paths.liveDir, 'CLAUDE.md'),
+        path.join(rendered.context.paths.liveDir, '.claude', 'CLAUDE.md'),
+        path.join(rendered.context.paths.liveDir, '.claude', 'agent-run-settings.json'),
+        path.join(rendered.context.paths.liveDir, '.claude', '.claude-plugin', 'plugin.json')
+    ]) {
+        if (!expectedFiles.has(path.resolve(filePath))) {
+            fs.rmSync(filePath, { force: true });
+        }
+    }
+    for (const name of ['git', 'git.cmd', 'npm', 'npm.cmd', 'pnpm', 'pnpm.cmd', 'gh', 'gh.cmd']) {
+        const filePath = path.join(rendered.context.paths.binDir, name);
+        if (!expectedFiles.has(path.resolve(filePath))) {
+            fs.rmSync(filePath, { force: true });
+        }
+    }
+    const skillNames = new Set(rendered.skills.map((skill) => skill.name));
+    removeStaleGeneratedSkills(rendered.context.paths.codexSkillsDir, rendered.context.tools.codex ? skillNames : new Set(), new Set(['.system']));
+    removeStaleGeneratedSkills(rendered.context.paths.claudeSkillsDir, rendered.context.tools.claude ? skillNames : new Set());
+}
+function removeStaleGeneratedSkills(dir, expectedNames, preservedNames = new Set()) {
+    if (!fs.existsSync(dir)) {
+        return;
+    }
+    for (const entry of fs.readdirSync(dir, { withFileTypes: true })) {
+        if (expectedNames.has(entry.name) || preservedNames.has(entry.name)) {
+            continue;
+        }
+        fs.rmSync(path.join(dir, entry.name), { recursive: true, force: true });
+    }
+}
+function removeLegacyGeneratedCodexFiles(context) {
+    for (const legacyPath of [
+        path.join(context.paths.liveDir, 'AGENTS.md'),
+        path.join(context.paths.liveDir, 'config.toml')
+    ]) {
+        if (!fs.existsSync(legacyPath)) {
+            continue;
+        }
+        fs.rmSync(legacyPath);
+        verbose(`removed legacy generated Codex file ${legacyPath}`);
+    }
+}
 function removeLegacyGeneratedClaudeSettings(context) {
     for (const legacyPath of [
         path.join(context.paths.liveDir, '.claude', 'settings.json'),
@@ -1459,8 +1549,24 @@ function renderClaudeSettings(env, configRoot, context, trace) {
         ? renderTemplateFile(env, configRoot, templatePath, context, trace)
         : defaultClaudeSettingsContent(context);
     assertNoUnexpandedTemplateVars('claude settings.json', content);
+    try {
+        JSON.parse(content);
+    }
+    catch (error) {
+        throw new Error(`invalid generated Claude settings JSON: ${formatError(error)}`);
+    }
     return content.replace(/\n*$/, '\n');
 }
+function claudePluginManifestContent(context) {
+    return `${JSON.stringify({
+        name: 'agent-run-profile',
+        description: `Generated skills for agent-run profile ${context.profile}`,
+        version: '1.0.0',
+        author: {
+            name: 'Technomoron'
+        }
+    }, null, 2)}\n`;
+}
 function resolveProfileOverrideTemplate(configRoot, context, overrideFileName, globalTemplatePath) {
     const overridePath = `${context.profile}/overrides/${overrideFileName}`;
     if (fs.existsSync(path.join(configRoot, overridePath))) {
@@ -1472,18 +1578,31 @@ function resolveProfileOverrideTemplate(configRoot, context, overrideFileName, g
     return null;
 }
 function renderGuardShims(context) {
+    const names = [];
+    if (context.guardrails.blockGitWrite) {
+        names.push('git');
+    }
+    if (context.guardrails.blockPublish) {
+        names.push('npm', 'pnpm');
+    }
+    if (context.guardrails.blockGithubRelease) {
+        names.push('gh');
+    }
     if (IS_WINDOWS) {
-        return ['git', 'npm', 'pnpm', 'gh'].map((name) => ({
+        return names.map((name) => ({
             path: path.join(context.paths.binDir, `${name}.cmd`),
             content: windowsShim(name)
         }));
     }
-    return [
-        { path: path.join(context.paths.binDir, 'git'), content: posixGitShim(), executable: true },
-        { path: path.join(context.paths.binDir, 'npm'), content: posixPublishShim('npm'), executable: true },
-        { path: path.join(context.paths.binDir, 'pnpm'), content: posixPublishShim('pnpm'), executable: true },
-        { path: path.join(context.paths.binDir, 'gh'), content: posixGhShim(), executable: true }
-    ];
+    return names.map((name) => ({
+        path: path.join(context.paths.binDir, name),
+        content: name === 'git'
+            ? posixGitShim()
+            : name === 'gh'
+                ? posixGhShim()
+                : posixPublishShim(name),
+        executable: true
+    }));
 }
 function syncRuntimeDirs(context) {
     for (const dir of [
@@ -1566,16 +1685,11 @@ function nextBackupPath(filePath) {
     return candidate;
 }
 function removeLegacyCodexSkillDirs(context) {
-    const legacyCodexSkillsDir = path.join(context.paths.liveDir, '.agents', 'skills');
-    if (path.resolve(legacyCodexSkillsDir) === path.resolve(context.paths.codexSkillsDir)) {
+    const legacyCodexDir = path.join(context.paths.liveDir, '.agents');
+    if (isSamePathOrDescendant(context.paths.codexSkillsDir, legacyCodexDir)) {
         return;
     }
-    for (const skill of context.skills) {
-        const legacySkillDir = path.join(legacyCodexSkillsDir, skill.name);
-        if (fs.existsSync(legacySkillDir)) {
-            fs.rmSync(legacySkillDir, { recursive: true, force: true });
-        }
-    }
+    fs.rmSync(legacyCodexDir, { recursive: true, force: true });
 }
 function removeLegacyCodeReviewSkillDirs(context) {
     if (!context.skills.some((skill) => skill.name === 'code-review-organizer')) {
@@ -1681,12 +1795,30 @@ function renderLegacyAgentsMods(sourceFile, stack = [], trace) {
     let sawLeadingInclude = false;
     let insertedOverrideNote = false;
     let contentStarted = false;
+    let fence = null;
     for (const line of lines) {
         const trimmed = line.trim();
+        const isIndentedCode = /^(?: {4}|\t)/.test(line);
+        const fenceMatch = isIndentedCode ? null : /^(`{3,}|~{3,})/.exec(trimmed);
+        if (fence !== null) {
+            output.push(line);
+            contentStarted = true;
+            const marker = fenceMatch?.[1];
+            if (marker !== undefined &&
+                marker[0] === fence.character &&
+                marker.length >= fence.length &&
+                trimmed.slice(marker.length).trim() === '') {
+                fence = null;
+            }
+            continue;
+        }
         if (!contentStarted && trimmed === '') {
             continue;
         }
-        if (trimmed.startsWith('@')) {
+        if (fenceMatch?.[1]) {
+            fence = { character: fenceMatch[1][0] ?? '`', length: fenceMatch[1].length };
+        }
+        if (fence === null && !isIndentedCode && trimmed.startsWith('@')) {
             const includePath = trimmed.slice(1).trim();
             if (!includePath) {
                 continue;
@@ -1739,28 +1871,39 @@ function checkProject(projectRoot) {
     const findings = [];
     verbose(`checking project ${projectRoot}`);
     const profileResult = resolveProfileResult(projectRoot);
-    const excludedDir = profileResult.profile === null ? null : resolveAgentDir(projectRoot);
-    const localAiFiles = findLocalAiFiles(projectRoot, excludedDir);
-    for (const file of localAiFiles) {
-        findings.push({ message: `local AI file in project: ${file}`, severity: 'ERROR' });
-    }
     if (profileResult.profile === null) {
+        for (const file of findLocalAiFiles(projectRoot, null)) {
+            findings.push({ message: `local AI file in project: ${file}`, severity: 'ERROR' });
+        }
         findings.push({ message: profileResult.reason, severity: 'ERROR' });
         return findings;
     }
     const agentDir = resolveAgentDir(projectRoot);
+    let forbidRepoAiFiles = true;
+    try {
+        const manifest = normalizeManifest(loadManifest(defaultConfigRoot(projectRoot), agentDir, profileResult.profile), profileResult.profile);
+        forbidRepoAiFiles = manifest.guardrails.forbidRepoAiFiles;
+    }
+    catch {
+        // The profile check below reports malformed or missing source details.
+    }
+    if (forbidRepoAiFiles) {
+        for (const file of findLocalAiFiles(projectRoot, agentDir)) {
+            findings.push({ message: `local AI file in project: ${file}`, severity: 'ERROR' });
+        }
+    }
     findings.push(...checkAgentDirectory(projectRoot, agentDir));
     return findings;
 }
 function checkAgentDirectory(projectRoot, agentDir) {
     const findings = [];
     const configRoot = defaultConfigRoot(projectRoot);
-    if (!fs.existsSync(path.join(agentDir, MANIFEST_FILE_NAME))) {
-        const legacyPath = path.join(agentDir, 'AGENTS-MODS.md');
-        const localPath = path.join(agentDir, LOCAL_TEMPLATE_FILE_NAME);
-        if (!fs.existsSync(legacyPath) && !fs.existsSync(localPath)) {
-            findings.push({ message: `missing manifest or legacy/local source file in ${agentDir}`, severity: 'ERROR' });
-        }
+    const manifestPath = path.join(agentDir, MANIFEST_FILE_NAME);
+    const legacyPath = path.join(agentDir, 'AGENTS-MODS.md');
+    const localPath = path.join(agentDir, LOCAL_TEMPLATE_FILE_NAME);
+    if (!fs.existsSync(manifestPath) && !fs.existsSync(legacyPath) && !fs.existsSync(localPath)) {
+        findings.push({ message: `missing manifest or legacy/local source file in ${agentDir}`, severity: 'ERROR' });
+        return findings;
     }
     for (const relativeTemplate of REQUIRED_GLOBAL_TEMPLATES) {
         if (!fs.existsSync(path.join(configRoot, relativeTemplate))) {
@@ -1779,20 +1922,26 @@ function checkSourceTree(rootPath) {
         findings: checkProject(projectRoot),
         label: projectRoot
     }));
-    return { entries, hasErrors: entries.some((entry) => hasErrors(entry.findings)), root: rootPath };
+    return { entries, hasErrors: entries.length === 0 || entries.some((entry) => hasErrors(entry.findings)), root: rootPath };
 }
 function findSourceRepos(rootPath) {
     const resolvedRoot = path.resolve(rootPath);
     const repos = new Set();
-    if (!isIgnoredDir(resolvedRoot) && looksLikeRepoRoot(resolvedRoot)) {
-        repos.add(resolvedRoot);
+    if (isIgnoredDir(resolvedRoot)) {
+        return [];
+    }
+    if (looksLikeRepoRoot(resolvedRoot)) {
+        return [resolvedRoot];
     }
-    walkSourceTree(resolvedRoot, 0, (fullPath, entry, depth) => {
-        if (entry.isDirectory() && entry.name === '.git') {
-            repos.add(path.dirname(fullPath));
+    walkSourceTree(resolvedRoot, 0, (fullPath, entry) => {
+        if (!entry.isDirectory()) {
+            return undefined;
+        }
+        if (shouldPruneSourceTreeEntry(entry) || isIgnoredDir(fullPath)) {
             return 'skip';
         }
-        if (entry.isDirectory() && depth >= 3) {
+        if (fs.existsSync(path.join(fullPath, '.git'))) {
+            repos.add(fullPath);
             return 'skip';
         }
         return undefined;
@@ -1802,6 +1951,12 @@ function findSourceRepos(rootPath) {
 function looksLikeRepoRoot(dir) {
     return fs.existsSync(path.join(dir, '.git')) || fs.existsSync(path.join(dir, 'package.json'));
 }
+function shouldPruneSourceTreeEntry(entry) {
+    return (entry.name === 'node_modules' ||
+        entry.name === '.pnpm-store' ||
+        entry.name === 'dist' ||
+        entry.name === 'build');
+}
 function printProjectReport(projectRoot, findings) {
     process.stdout.write(`Check: ${projectRoot}\n`);
     if (findings.length === 0) {
@@ -1816,7 +1971,7 @@ function printProjectReport(projectRoot, findings) {
 function printBatchReport(rootPath, entries) {
     process.stdout.write(`Check all: ${rootPath}\n`);
     if (entries.length === 0) {
-        process.stdout.write('WARN no source repos found\n');
+        process.stdout.write('ERROR no source repos found\n');
         return;
     }
     let totalErrors = 0;
@@ -1847,86 +2002,80 @@ function countWarnings(findings) {
 function formatError(error) {
     return error instanceof Error ? error.message : String(error);
 }
-function runCodex(realBinary, permissionArgs, agentDir, configRoot, args, projectRoot, wrapperArgs) {
-    const liveDir = profileLiveDir(agentDir);
-    const agentsPath = path.join(liveDir, 'AGENTS.md');
+function runCodex(realBinary, permissionArgs, context, args, wrapperArgs) {
+    const liveDir = context.paths.liveDir;
+    const codexHomeDir = context.paths.codexHomeDir;
+    const projectRoot = context.projectRoot;
+    const agentsPath = path.join(codexHomeDir, 'AGENTS.md');
     if (!fs.existsSync(agentsPath)) {
-        failMissingConfig('codex', agentDir);
+        failMissingConfig('codex', context.profileDir);
     }
     const guardBin = path.join(liveDir, 'bin');
-    const codexHomeDir = path.join(liveDir, 'memories', 'codex-home');
+    const realPath = process.env.AGENT_RUN_REAL_PATH ?? process.env.PATH ?? '';
     fs.mkdirSync(codexHomeDir, { recursive: true });
     const env = {
         ...process.env,
         CODEX_HOME: codexHomeDir,
         AGENT_DIR: liveDir,
-        AGENT_PROFILE_DIR: agentDir,
+        AGENT_PROFILE_DIR: context.profileDir,
         AGENT_RUN_PROJECT_ROOT: projectRoot,
-        PATH: `${guardBin}${path.delimiter}${process.env.PATH ?? ''}`
+        AGENT_RUN_REAL_PATH: realPath,
+        PATH: `${guardBin}${path.delimiter}${realPath}`
     };
     const codexRuntimeArgs = buildCodexRuntimeArgs(wrapperArgs);
     execCommand(realBinary, [
         ...permissionArgs,
         ...codexRuntimeArgs,
-        '--config',
-        `system_prompt_file=${agentsPath}`,
-        '--config',
-        'project_doc_max_bytes=65536',
-        ...globalMemoryArgs(configRoot),
         '-C',
         projectRoot,
-        ...(wrapperArgs.codexSandboxMode === 'sandboxed' && wrapperArgs.codexNetwork
+        ...(wrapperArgs.codexSandboxMode !== 'danger' && wrapperArgs.codexNetwork
             ? ['--config', 'sandbox_workspace_write.network_access=true']
             : []),
         ...args
-    ], shouldUseShell(realBinary), env, codexHomeDir, (code) => postflightProjectCheck(projectRoot, agentDir, wrapperArgs.local, code));
+    ], env, codexHomeDir, (code) => postflightProjectCheck(projectRoot, context.profileDir, context.guardrails.forbidRepoAiFiles, wrapperArgs.local, code));
 }
 function buildCodexRuntimeArgs(wrapperArgs) {
-    const mode = wrapperArgs.codexSandboxMode ?? 'danger';
-    if (mode === 'sandboxed') {
-        return ['-s', 'workspace-write'];
+    if (wrapperArgs.codexSandboxMode === 'danger') {
+        return ['-a', 'never', '-s', 'danger-full-access'];
     }
-    return ['-a', 'never', '-s', 'danger-full-access'];
+    return ['-a', 'on-request', '-s', 'workspace-write'];
 }
-function runClaude(realBinary, permissionArgs, agentDir, configRoot, args, projectRoot, wrapperArgs) {
-    const liveDir = profileLiveDir(agentDir);
+function runClaude(realBinary, permissionArgs, context, args, wrapperArgs) {
+    const liveDir = context.paths.liveDir;
+    const projectRoot = context.projectRoot;
     const claudePath = path.join(liveDir, 'CLAUDE.md');
     if (!fs.existsSync(claudePath)) {
-        failMissingConfig('claude', agentDir);
+        failMissingConfig('claude', context.profileDir);
     }
     const guardBin = path.join(liveDir, 'bin');
     const claudeConfigDir = path.join(liveDir, '.claude');
+    const realPath = process.env.AGENT_RUN_REAL_PATH ?? process.env.PATH ?? '';
     const env = {
         ...process.env,
-        CLAUDE_CONFIG_DIR: claudeConfigDir,
         AGENT_DIR: liveDir,
-        AGENT_PROFILE_DIR: agentDir,
+        AGENT_PROFILE_DIR: context.profileDir,
         AGENT_RUN_PROJECT_ROOT: projectRoot,
-        PATH: `${guardBin}${path.delimiter}${process.env.PATH ?? ''}`
+        AGENT_RUN_REAL_PATH: realPath,
+        PATH: `${guardBin}${path.delimiter}${realPath}`
     };
     execCommand(realBinary, [
         ...permissionArgs,
+        '--append-system-prompt-file',
+        claudePath,
         '--settings',
         path.join(claudeConfigDir, 'agent-run-settings.json'),
-        '--add-dir',
-        projectRoot,
-        '--add-dir',
-        liveDir,
-        ...globalMemoryArgs(configRoot),
+        '--plugin-dir',
+        claudeConfigDir,
         ...args
-    ], shouldUseShell(realBinary), env, projectRoot, (code) => postflightProjectCheck(projectRoot, agentDir, wrapperArgs.local, code));
-}
-function profileLiveDir(agentDir) {
-    return path.join(agentDir, LIVE_DIR_NAME);
-}
-function globalMemoryArgs(configRoot) {
-    const memoryDir = globalMemoryDir(configRoot);
-    return fs.existsSync(memoryDir) ? ['--add-dir', memoryDir] : [];
+    ], env, projectRoot, (code) => postflightProjectCheck(projectRoot, context.profileDir, context.guardrails.forbidRepoAiFiles, wrapperArgs.local, code));
 }
 function globalMemoryDir(configRoot) {
     return path.join(configRoot, 'notes', 'memory');
 }
-function postflightProjectCheck(projectRoot, agentDir, allowLocal, code) {
+function postflightProjectCheck(projectRoot, agentDir, forbidRepoAiFiles, allowLocal, code) {
+    if (!forbidRepoAiFiles) {
+        return code;
+    }
     const localAiFiles = findLocalAiFiles(projectRoot, agentDir);
     if (localAiFiles.length > 0) {
         warnForLocalAiFiles(null, projectRoot, localAiFiles);
@@ -2014,17 +2163,16 @@ function isSamePathOrDescendant(candidatePath, parentPath) {
 function shouldPruneProjectEntry(entry) {
     return (entry.isDirectory() &&
         (entry.name === '.git' ||
-            entry.name === '.claude' ||
             entry.name === 'node_modules' ||
             entry.name === '.pnpm-store' ||
             entry.name === 'dist' ||
             entry.name === 'build'));
 }
 function isLocalAiDirectory(entry) {
-    return entry.isDirectory() && (entry.name === '.claude' || entry.name === '.codex' || entry.name === '.agents');
+    return LOCAL_AI_DIRECTORY_NAMES.has(entry.name);
 }
 function isLocalAiFile(entry) {
-    return entry.isFile() && LOCAL_AI_FILE_NAMES.has(entry.name);
+    return LOCAL_AI_FILE_NAMES.has(entry.name);
 }
 function isIgnoredDir(dir) {
     if (fs.existsSync(path.join(dir, IGNORE_FILE_NAME))) {
@@ -2057,13 +2205,13 @@ function findProjectRoot(cwd) {
     let gitRoot = '';
     for (;;) {
         const packagePath = path.join(dir, 'package.json');
+        if (isWorkspaceRoot(dir)) {
+            workspaceRoot = dir;
+        }
         if (fs.existsSync(packagePath)) {
             if (!nearestPackageRoot) {
                 nearestPackageRoot = dir;
             }
-            if (isWorkspaceRoot(dir)) {
-                workspaceRoot = dir;
-            }
         }
         if (fs.existsSync(path.join(dir, '.git'))) {
             gitRoot = dir;
@@ -2137,26 +2285,16 @@ function resolveGitHubProfile(projectRoot) {
     return remote === null ? null : parseGitHubRemoteProfile(remote);
 }
 function readGitOrigin(projectRoot) {
-    const configPath = path.join(projectRoot, '.git', 'config');
-    if (!fs.existsSync(configPath)) {
+    const result = childProcess.spawnSync('git', ['-C', projectRoot, 'config', '--get', 'remote.origin.url'], {
+        encoding: 'utf8',
+        shell: false,
+        stdio: ['ignore', 'pipe', 'ignore']
+    });
+    if (result.status !== 0) {
         return null;
     }
-    const lines = fs.readFileSync(configPath, 'utf8').replace(/\r\n/g, '\n').split('\n');
-    let inOrigin = false;
-    for (const line of lines) {
-        const trimmed = line.trim();
-        if (trimmed.startsWith('[')) {
-            inOrigin = trimmed === '[remote "origin"]';
-            continue;
-        }
-        if (inOrigin && trimmed.startsWith('url')) {
-            const equalsIndex = trimmed.indexOf('=');
-            if (equalsIndex >= 0) {
-                return trimmed.slice(equalsIndex + 1).trim();
-            }
-        }
-    }
-    return null;
+    const remote = result.stdout.trim();
+    return remote || null;
 }
 function parseGitHubRemoteProfile(remote) {
     const patterns = [
@@ -2181,7 +2319,8 @@ function parseProfile(profile, source) {
         return { profile: null, reason: `${source} must be relative to the config root, not an absolute path` };
     }
     const segments = normalized.split('/').filter((segment) => segment.length > 0);
-    if (segments.length === 0 || segments.some((segment) => segment === '.' || segment === '..')) {
+    if (segments.length === 0 ||
+        segments.some((segment) => segment === '.' || segment === '..' || !/^[A-Za-z0-9._-]+$/.test(segment))) {
         return { profile: null, reason: `${source} must be a clean relative path like org/my-project` };
     }
     return { profile: segments.join('/'), reason: '' };
@@ -2232,7 +2371,7 @@ function parseBooleanEnv(value) {
     const normalized = value.trim().toLowerCase();
     return normalized === '1' || normalized === 'true' || normalized === 'yes' || normalized === 'on';
 }
-function defaultConfigRoot(projectRoot) {
+function defaultConfigRoot(projectRoot, options = {}) {
     const overrideRoot = process.env[CONFIG_ROOT_OVERRIDE_ENV];
     if (overrideRoot) {
         return path.resolve(overrideRoot);
@@ -2255,9 +2394,15 @@ function defaultConfigRoot(projectRoot) {
         }
     }
     if (projectRoot) {
-        return defaultCodeConfigRoot(projectRoot);
+        const projectConfigRoot = defaultCodeConfigRoot(projectRoot);
+        if (options.preferProjectRoot || fs.existsSync(projectConfigRoot)) {
+            return projectConfigRoot;
+        }
+        const discoveredConfigRoot = findExistingConfigRoot(defaultConfigRootSearchCandidates());
+        return discoveredConfigRoot ?? projectConfigRoot;
     }
-    return path.join(os.homedir(), '.agent-config');
+    const discoveredConfigRoot = findExistingConfigRoot(defaultConfigRootSearchCandidates());
+    return discoveredConfigRoot ?? path.join(os.homedir(), '.agent-config');
 }
 function defaultCodeConfigRoot(projectRoot) {
     const resolvedProjectRoot = path.resolve(projectRoot);
@@ -2268,6 +2413,39 @@ function defaultCodeConfigRoot(projectRoot) {
     }
     return path.join(codeRoot, 'agent-config');
 }
+function findExistingConfigRoot(candidates) {
+    for (const candidate of candidates) {
+        if (fs.existsSync(candidate)) {
+            return candidate;
+        }
+    }
+    return null;
+}
+function defaultConfigRootSearchCandidates(_projectRoot, options = {}) {
+    const platform = options.platform ?? process.platform;
+    const pathApi = platform === 'win32' ? path.win32 : path.posix;
+    const homeDir = options.homeDir ?? os.homedir();
+    const configNames = ['agent-config', 'agent-configs'];
+    const candidates = [];
+    if (platform === 'win32') {
+        for (const codeRoot of [pathApi.join(homeDir, 'Documents', 'code'), pathApi.join(homeDir, 'Desktop', 'code'), 'C:\\code']) {
+            for (const configName of configNames) {
+                candidates.push(pathApi.join(codeRoot, configName));
+            }
+        }
+        return candidates;
+    }
+    for (const configName of configNames) {
+        candidates.push(pathApi.join(homeDir, 'code', configName));
+    }
+    for (const configName of configNames) {
+        candidates.push(pathApi.join(homeDir, configName));
+    }
+    for (const configName of configNames) {
+        candidates.push(pathApi.join(homeDir, `.${configName}`));
+    }
+    return candidates;
+}
 function findRealBinary(tool) {
     const pathValue = process.env.PATH || '';
     const pathDirs = pathValue.split(path.delimiter).filter((entry) => entry.length > 0);
@@ -2360,12 +2538,12 @@ function isExecutable(filePath) {
     }
 }
 function execTool(command, args) {
-    verbose(`exec tool: ${formatCommand(command, args)} shell=${String(shouldUseShell(command))}`);
-    execCommand(command, args, shouldUseShell(command));
+    verbose(`exec tool: ${formatCommand(command, args)}`);
+    execCommand(command, args);
 }
-function execCommand(command, args, shell, env, cwd, onExit) {
-    verbose(`spawn: ${formatCommand(command, args)} shell=${String(shell)} cwd=${cwd ?? process.cwd()}`);
-    const child = childProcess.spawn(command, args, { cwd, env, shell, stdio: 'inherit' });
+function execCommand(command, args, env, cwd, onExit) {
+    verbose(`spawn: ${formatCommand(command, args)} cwd=${cwd ?? process.cwd()}`);
+    const child = crossSpawn(command, args, { cwd, env, stdio: 'inherit' });
     child.on('exit', (code, signal) => {
         if (signal) {
             process.kill(process.pid, signal);
@@ -2381,33 +2559,106 @@ function execCommand(command, args, shell, env, cwd, onExit) {
 function openEditor(filePath) {
     const visual = process.env.VISUAL?.trim();
     if (visual) {
-        execCommand(visual, [filePath], true);
+        runConfiguredEditor(visual, filePath);
         return;
     }
     const editor = process.env.EDITOR?.trim();
     if (editor) {
-        execCommand(editor, [filePath], true);
+        runConfiguredEditor(editor, filePath);
         return;
     }
     const vscodeCommand = findVsCodeEditorCommand();
     if (vscodeCommand !== null) {
-        execCommand(vscodeCommand, ['--reuse-window', filePath], shouldUseShell(vscodeCommand));
+        execCommand(vscodeCommand, ['--reuse-window', filePath]);
         return;
     }
     const fallbackEditor = findFallbackEditor();
     if (fallbackEditor !== null) {
-        execCommand(fallbackEditor, [filePath], shouldUseShell(fallbackEditor));
+        execCommand(fallbackEditor, [filePath]);
         return;
     }
     if (IS_WINDOWS) {
-        execCommand('cmd.exe', ['/c', 'start', '', filePath], false);
+        execCommand('explorer.exe', [filePath]);
         return;
     }
     if (process.platform === 'darwin') {
-        execCommand('open', [filePath], false);
+        execCommand('open', [filePath]);
         return;
     }
-    execCommand('xdg-open', [filePath], false);
+    execCommand('xdg-open', [filePath]);
+}
+function runConfiguredEditor(commandLine, filePath) {
+    let editorArgs;
+    try {
+        editorArgs = parseEditorCommand(commandLine);
+    }
+    catch (error) {
+        fail(`invalid editor command: ${formatError(error)}`);
+    }
+    const [command, ...args] = editorArgs;
+    if (!command) {
+        fail('invalid editor command: command is empty');
+    }
+    execCommand(command, [...args, filePath]);
+}
+function parseEditorCommand(commandLine) {
+    const args = [];
+    let current = '';
+    let quote = null;
+    let tokenStarted = false;
+    for (let index = 0; index < commandLine.length; index += 1) {
+        const character = commandLine[index] ?? '';
+        if (quote !== null) {
+            if (character === quote) {
+                quote = null;
+                continue;
+            }
+            if (character === '\\' && quote === '"') {
+                const next = commandLine[index + 1];
+                if (next === '"' || next === '\\') {
+                    current += next;
+                    index += 1;
+                    continue;
+                }
+            }
+            current += character;
+            continue;
+        }
+        if (character === "'" || character === '"') {
+            quote = character;
+            tokenStarted = true;
+            continue;
+        }
+        if (/\s/.test(character)) {
+            if (tokenStarted) {
+                args.push(current);
+                current = '';
+                tokenStarted = false;
+            }
+            continue;
+        }
+        if (character === '\\') {
+            const next = commandLine[index + 1];
+            if (next !== undefined && (/\s/.test(next) || next === "'" || next === '"' || next === '\\')) {
+                current += next;
+                index += 1;
+                tokenStarted = true;
+                continue;
+            }
+        }
+        current += character;
+        tokenStarted = true;
+    }
+    if (quote !== null) {
+        throw new Error(`unterminated ${quote} quote`);
+    }
+    if (tokenStarted) {
+        args.push(current);
+    }
+    if (args.length === 0) {
+        throw new Error('command is empty');
+    }
+    return args;
 }
 function findVsCodeEditorCommand() {
     if (!isRunningInVsCodeTerminal()) {
@@ -2452,13 +2703,6 @@ function findExecutable(command) {
     }
     return null;
 }
-function shouldUseShell(command) {
-    if (!IS_WINDOWS) {
-        return false;
-    }
-    const extension = path.extname(command).toLowerCase();
-    return extension === '.cmd' || extension === '.bat';
-}
 function localDateString() {
     const now = new Date();
     const year = String(now.getFullYear()).padStart(4, '0');
@@ -2608,7 +2852,8 @@ function defaultReleasePackageCheckSkill() {
         '- The current branch has an upstream configured and is in sync with it after fetching.',
         '- The repository does not contain agent files or directories such as `AGENTS.md`, `CLAUDE.md`, `codex.md`, `.claude`, or `.codex`.',
         '- The repository root has a lockfile: `pnpm-lock.yaml`, `package-lock.json`, `yarn.lock`, `bun.lockb`, or `bun.lock`.',
-        '- GitHub workflows under `.github/workflows` use `actions/setup-node@v6` and `node-version: 24`.',
+        '- Every GitHub Actions `uses:` reference is pinned to a full commit SHA.',
+        '- The pinned `actions/setup-node` release is v6-compatible and workflows use `node-version: 24`.',
         '- GitHub workflows do not reference `node20` or `node22`.',
         '- The git working tree is clean for files under the checked package directory.',
         '- If files beyond `CHANGES` changed in the checked package directory, that package `CHANGES` file is also changed.',
@@ -2724,8 +2969,8 @@ function defaultToolInstructionsTemplate(isClaude) {
         '## Tool Note',
         '',
         isClaude
-            ? 'Claude uses the generated config directory under {{ paths.liveDir }}/.claude and may read {{ paths.liveDir }} via `--add-dir`.'
-            : 'Codex uses {{ agentDir }}/AGENTS.md as `system_prompt_file` and {{ paths.codexHomeDir }} as CODEX_HOME.',
+            ? 'Claude receives {{ agentDir }}/CLAUDE.md through `--append-system-prompt-file` and loads generated skills as a local plugin.'
+            : 'Codex loads AGENTS.md, config.toml, and skills natively from {{ paths.codexHomeDir }}.',
         '',
         '## Mandatory Path Rule',
         '',
@@ -2740,14 +2985,14 @@ function defaultCodexConfigTemplate() {
         '# Generated by agent-run. Do not edit directly.',
         '',
         'project_doc_max_bytes = 65536',
+        'approval_policy = "on-request"',
         'sandbox_mode = "workspace-write"',
         '',
         '[sandbox_workspace_write]',
         'writable_roots = [',
-        '  "{{ projectRoot }}",',
-        '  "{{ agentDir }}",',
-        '  "{{ profileDir }}",',
-        '  "{{ paths.globalMemoryDir }}"',
+        '  {{ projectRoot | dump }},',
+        '  {{ paths.reviewDir | dump }},',
+        '  {{ paths.memoriesDir | dump }}',
         ']',
         'network_access = false',
         ''
@@ -2756,19 +3001,17 @@ function defaultCodexConfigTemplate() {
 function defaultClaudeSettingsTemplate() {
     const envBlock = [
         '  "env": {',
-        '    "AGENT_DIR": "{{ agentDir }}",',
-        '    "AGENT_PROFILE_DIR": "{{ profileDir }}",',
-        '    "AGENT_RUN_PROJECT_ROOT": "{{ projectRoot }}",',
-        '    "AGENT_GLOBAL_MEMORY_DIR": "{{ paths.globalMemoryDir }}"',
+        '    "AGENT_DIR": {{ agentDir | dump }},',
+        '    "AGENT_PROFILE_DIR": {{ profileDir | dump }},',
+        '    "AGENT_RUN_PROJECT_ROOT": {{ projectRoot | dump }},',
+        '    "AGENT_GLOBAL_MEMORY_DIR": {{ paths.globalMemoryDir | dump }}',
         '  }'
     ].join('\n');
     return [
         '{% if permissionsAllow.length %}{',
         envBlock + ',',
         '  "permissions": {',
-        '    "allow": [',
-        '      "{{ permissionsAllow | join(\'",\\n      "\') }}"',
-        '    ]',
+        '    "allow": {{ permissionsAllow | dump }}',
         '  }',
         '}',
         '{% else %}{',
@@ -2782,14 +3025,14 @@ function defaultCodexConfigContent(context) {
         '# Generated by agent-run. Do not edit directly.',
         '',
         'project_doc_max_bytes = 65536',
+        'approval_policy = "on-request"',
         'sandbox_mode = "workspace-write"',
         '',
         '[sandbox_workspace_write]',
         'writable_roots = [',
         `  ${jsonString(context.projectRoot)},`,
-        `  ${jsonString(context.agentDir)},`,
-        `  ${jsonString(context.profileDir)},`,
-        `  ${jsonString(context.paths.globalMemoryDir)}`,
+        `  ${jsonString(context.paths.reviewDir)},`,
+        `  ${jsonString(context.paths.memoriesDir)}`,
         ']',
         'network_access = false',
         ''
@@ -2825,18 +3068,17 @@ function posixGitShim() {
     return [
         '#!/usr/bin/env bash',
         'set -euo pipefail',
-        'case "${1:-}" in',
-        '  commit|tag|push)',
-        '    if [ "${AGENT_RUN_ALLOW_GIT_WRITE:-}" != "1" ]; then',
-        '      echo "agent-run: blocked git $1. Review and run it manually, or set AGENT_RUN_ALLOW_GIT_WRITE=1 for this invocation." >&2',
-        '      exit 42',
-        '    fi',
-        '    ;;',
-        'esac',
-        'if command -v /usr/bin/git >/dev/null 2>&1; then',
-        '  exec /usr/bin/git "$@"',
-        'fi',
-        'exec git "$@"',
+        'for arg in "$@"; do',
+        '  case "$arg" in',
+        '    commit|tag|push)',
+        '      if [ "${AGENT_RUN_ALLOW_GIT_WRITE:-}" != "1" ]; then',
+        '        echo "agent-run: blocked git $arg. Review and run it manually, or set AGENT_RUN_ALLOW_GIT_WRITE=1 for this invocation." >&2',
+        '        exit 42',
+        '      fi',
+        '      ;;',
+        '  esac',
+        'done',
+        ...posixRunRealCommand('git'),
         ''
     ].join('\n');
 }
@@ -2844,14 +3086,13 @@ function posixPublishShim(tool) {
     return [
         '#!/usr/bin/env bash',
         'set -euo pipefail',
-        'if [ "${1:-}" = "publish" ] && [ "${AGENT_RUN_ALLOW_PUBLISH:-}" != "1" ]; then',
-        `  echo "agent-run: blocked ${tool} publish. Review and run it manually, or set AGENT_RUN_ALLOW_PUBLISH=1 for this invocation." >&2`,
-        '  exit 42',
-        'fi',
-        `if command -v /usr/bin/${tool} >/dev/null 2>&1; then`,
-        `  exec /usr/bin/${tool} "$@"`,
-        'fi',
-        `exec ${tool} "$@"`,
+        'for arg in "$@"; do',
+        '  if [ "$arg" = "publish" ] && [ "${AGENT_RUN_ALLOW_PUBLISH:-}" != "1" ]; then',
+        `    echo "agent-run: blocked ${tool} publish. Review and run it manually, or set AGENT_RUN_ALLOW_PUBLISH=1 for this invocation." >&2`,
+        '    exit 42',
+        '  fi',
+        'done',
+        ...posixRunRealCommand(tool),
         ''
     ].join('\n');
 }
@@ -2859,44 +3100,95 @@ function posixGhShim() {
     return [
         '#!/usr/bin/env bash',
         'set -euo pipefail',
-        'if [ "${1:-}" = "release" ] && [ "${2:-}" = "create" ] && [ "${AGENT_RUN_ALLOW_GITHUB_RELEASE:-}" != "1" ]; then',
-        '  echo "agent-run: blocked gh release create. Review and run it manually, or set AGENT_RUN_ALLOW_GITHUB_RELEASE=1 for this invocation." >&2',
-        '  exit 42',
-        'fi',
-        'if command -v /usr/bin/gh >/dev/null 2>&1; then',
-        '  exec /usr/bin/gh "$@"',
-        'fi',
-        'exec gh "$@"',
+        'saw_release=0',
+        'for arg in "$@"; do',
+        '  if [ "$arg" = "release" ]; then',
+        '    saw_release=1',
+        '  elif [ "$saw_release" = "1" ] && [ "$arg" = "create" ] && [ "${AGENT_RUN_ALLOW_GITHUB_RELEASE:-}" != "1" ]; then',
+        '    echo "agent-run: blocked gh release create. Review and run it manually, or set AGENT_RUN_ALLOW_GITHUB_RELEASE=1 for this invocation." >&2',
+        '    exit 42',
+        '  fi',
+        'done',
+        ...posixRunRealCommand('gh'),
         ''
     ].join('\n');
 }
+function posixRunRealCommand(tool) {
+    return [
+        'shim_dir="$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd -P)"',
+        'real_path="${AGENT_RUN_REAL_PATH:-}"',
+        'if [ -z "$real_path" ]; then',
+        '  case "${PATH:-}" in',
+        '    "$shim_dir") real_path="" ;;',
+        '    "$shim_dir":*) real_path="${PATH#*:}" ;;',
+        '    *) real_path="${PATH:-}" ;;',
+        '  esac',
+        'fi',
+        `real_command="$(PATH="$real_path" command -v ${tool} || true)"`,
+        'if [ -z "$real_command" ]; then',
+        `  echo "agent-run: cannot find the real ${tool} command outside the guard directory." >&2`,
+        '  exit 127',
+        'fi',
+        `if [ "$real_command" = "$shim_dir/${tool}" ]; then`,
+        `  echo "agent-run: refused recursive ${tool} guard resolution." >&2`,
+        '  exit 127',
+        'fi',
+        'PATH="$real_path" exec "$real_command" "$@"'
+    ];
+}
 function windowsShim(name) {
+    const executable = name === 'npm' || name === 'pnpm' ? `${name}.cmd` : `${name}.exe`;
     const guard = name === 'git'
         ? [
-            'if /I "%1"=="commit" goto block_git',
-            'if /I "%1"=="tag" goto block_git',
-            'if /I "%1"=="push" goto block_git',
-            'goto run',
+            ':scan',
+            'if "%~1"=="" goto run',
+            'if /I "%~1"=="commit" goto block_git',
+            'if /I "%~1"=="tag" goto block_git',
+            'if /I "%~1"=="push" goto block_git',
+            'shift',
+            'goto scan',
             ':block_git',
             'if "%AGENT_RUN_ALLOW_GIT_WRITE%"=="1" goto run',
-            'echo agent-run: blocked git %1. Review and run it manually, or set AGENT_RUN_ALLOW_GIT_WRITE=1 for this invocation. 1>&2',
+            'echo agent-run: blocked git write. Review and run it manually, or set AGENT_RUN_ALLOW_GIT_WRITE=1 for this invocation. 1>&2',
             'exit /b 42'
         ]
         : name === 'gh'
             ? [
-                'if /I not "%1"=="release" goto run',
-                'if /I not "%2"=="create" goto run',
+                'set "SAW_RELEASE=0"',
+                ':scan',
+                'if "%~1"=="" goto run',
+                'if /I "%~1"=="release" set "SAW_RELEASE=1"',
+                'if "%SAW_RELEASE%"=="1" if /I "%~1"=="create" goto block_release',
+                'shift',
+                'goto scan',
+                ':block_release',
                 'if "%AGENT_RUN_ALLOW_GITHUB_RELEASE%"=="1" goto run',
                 'echo agent-run: blocked gh release create. Review and run it manually, or set AGENT_RUN_ALLOW_GITHUB_RELEASE=1 for this invocation. 1>&2',
                 'exit /b 42'
             ]
             : [
-                'if /I not "%1"=="publish" goto run',
+                ':scan',
+                'if "%~1"=="" goto run',
+                'if /I "%~1"=="publish" goto block_publish',
+                'shift',
+                'goto scan',
+                ':block_publish',
                 'if "%AGENT_RUN_ALLOW_PUBLISH%"=="1" goto run',
                 `echo agent-run: blocked ${name} publish. Review and run it manually, or set AGENT_RUN_ALLOW_PUBLISH=1 for this invocation. 1>&2`,
                 'exit /b 42'
             ];
-    return ['@echo off', ...guard, ':run', `${name}.exe %*`, ''].join('\n');
+    return [
+        '@echo off',
+        ...guard,
+        ':run',
+        'if defined AGENT_RUN_REAL_PATH (',
+        '  set "PATH=%AGENT_RUN_REAL_PATH%"',
+        ') else (',
+        '  for /f "tokens=1,* delims=;" %%A in ("%PATH%") do set "PATH=%%B"',
+        ')',
+        `${executable} %*`,
+        ''
+    ].join('\n');
 }
 function isVerbose() {
     return parseBooleanEnv(process.env[VERBOSE_ENV]);