@technomoron/agent-run 0.99.12 → 0.99.13

package/CHANGES

@@ -1,8 +1,9 @@
 CHANGES
 =======
 
-Unreleased (2026-04-24)
------------------------
+Version 0.99.13 (2026-04-27)
+----------------------------
+* Render each profile's generated files and runtime state under `live/`, leaving the profile root for source config and templates.
 
 Version 0.99.12 (2026-04-27)
 ----------------------------

package/dist/agent-run.js

@@ -22,28 +22,13 @@ 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 = '0.99.10';
 const UNEXPANDED_TEMPLATE_RE = /\{\{[^}]+\}\}|\{%[^%]+%\}/;
 const agentRunEnvCache = new Map();
 const GENERATED_GITIGNORE_ENTRIES = [
-    '# Generated agent-run files',
-    '**/AGENTS.md',
-    '**/CLAUDE.md',
-    '**/GEMINI.md',
-    '**/config.toml',
-    '',
-    '# Generated native agent homes',
-    '**/.agents/',
-    '**/.claude/',
-    '**/.codex/',
-    '',
-    '# Generated runtime files',
-    '**/bin/',
-    '**/reviews/',
-    '**/memories/',
-    '',
-    '# Generated review reports',
-    '**/REVIEW-*.md',
+    '# Generated agent-run live profiles',
+    '**/live/',
     '',
     '# Optional generated caches',
     '**/.agent-run-cache/'
@@ -670,7 +655,8 @@ function runCheck(parsed) {
 }
 function printUpdateSummary(rendered) {
     process.stdout.write(`OK profile ${rendered.profile}\n`);
-    process.stdout.write(`Agent dir: ${rendered.agentDir}\n`);
+    process.stdout.write(`Profile dir: ${rendered.agentDir}\n`);
+    process.stdout.write(`Live dir: ${rendered.context.paths.liveDir}\n`);
     process.stdout.write(`Generated files: ${rendered.files.length}\n`);
     process.stdout.write(`Installed skills: ${rendered.skills.map((skill) => skill.name).join(', ') || '(none)'}\n`);
 }
@@ -992,29 +978,33 @@ function createNunjucksEnv(configRoot) {
         throwOnUndefined: true
     });
 }
-function buildRenderContext(projectRoot, agentDir, configRoot, manifest, env) {
+function buildRenderContext(projectRoot, profileDir, configRoot, manifest, env) {
     const date = localDateString();
+    const liveDir = path.join(profileDir, LIVE_DIR_NAME);
     const baseContext = {
         profile: manifest.profile,
         kind: manifest.kind,
         projectRoot,
-        agentDir,
+        agentDir: liveDir,
+        profileDir,
         configRoot,
         date,
         checks: manifest.checks,
         guardrails: manifest.guardrails
     };
     const paths = {
+        profileDir,
+        liveDir,
         changesFile: resolveRuntimePath(configRoot, manifest.paths.changesFile, env, baseContext),
         reviewDir: resolveRuntimePath(configRoot, manifest.paths.reviewDir, env, baseContext),
         reviewFile: resolveRuntimePath(configRoot, manifest.paths.reviewFile, env, baseContext),
         memoriesDir: resolveRuntimePath(configRoot, manifest.paths.memoriesDir, env, baseContext),
         globalMemoryDir: globalMemoryDir(configRoot),
         codexHomeDir: path.join(resolveRuntimePath(configRoot, manifest.paths.memoriesDir, env, baseContext), 'codex-home'),
-        overridesDir: path.join(agentDir, 'overrides'),
-        codexSkillsDir: path.join(agentDir, '.agents', 'skills'),
-        claudeSkillsDir: path.join(agentDir, '.claude', 'skills'),
-        binDir: path.join(agentDir, 'bin')
+        overridesDir: path.join(profileDir, 'overrides'),
+        codexSkillsDir: path.join(liveDir, '.agents', 'skills'),
+        claudeSkillsDir: path.join(liveDir, '.claude', 'skills'),
+        binDir: path.join(liveDir, 'bin')
     };
     return {
         ...baseContext,
@@ -1135,11 +1125,14 @@ function renderProfile(projectRoot, agentDir, checkOnly = false) {
     const files = [];
     const agentsContent = renderToolInstructions('AGENTS.md', env, configRoot, context, false);
     const claudeContent = renderToolInstructions('CLAUDE.md', env, configRoot, context, true);
-    files.push({ path: path.join(agentDir, 'AGENTS.md'), content: agentsContent });
-    files.push({ path: path.join(agentDir, 'CLAUDE.md'), content: claudeContent });
-    files.push({ path: path.join(agentDir, '.claude', 'CLAUDE.md'), content: claudeContent });
-    files.push({ path: path.join(agentDir, 'config.toml'), content: renderCodexConfig(env, configRoot, context) });
-    files.push({ path: path.join(agentDir, '.claude', 'agent-run-settings.json'), content: renderClaudeSettings(env, configRoot, context) });
+    files.push({ path: path.join(context.paths.liveDir, 'AGENTS.md'), content: agentsContent });
+    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, 'config.toml'), content: renderCodexConfig(env, configRoot, context) });
+    files.push({
+        path: path.join(context.paths.liveDir, '.claude', 'agent-run-settings.json'),
+        content: renderClaudeSettings(env, configRoot, context)
+    });
     files.push(...renderNativeSkillFiles(context));
     files.push(...renderGuardShims(context));
     return {
@@ -1161,15 +1154,22 @@ function syncAgentProfile(projectRoot, agentDir) {
     return rendered;
 }
 function removeLegacyGeneratedClaudeSettings(context) {
-    const legacyPath = path.join(context.agentDir, '.claude', 'settings.json');
-    if (!fs.existsSync(legacyPath)) {
-        return;
-    }
-    const actual = fs.readFileSync(legacyPath, 'utf8').replace(/\r\n/g, '\n');
-    const legacyGeneratedContent = legacyDefaultClaudeSettingsContent(context);
-    if (actual === legacyGeneratedContent) {
-        fs.rmSync(legacyPath);
-        verbose(`removed legacy generated Claude settings ${legacyPath}`);
+    for (const legacyPath of [
+        path.join(context.paths.liveDir, '.claude', 'settings.json'),
+        path.join(context.profileDir, '.claude', 'settings.json')
+    ]) {
+        if (!fs.existsSync(legacyPath)) {
+            continue;
+        }
+        const actual = fs.readFileSync(legacyPath, 'utf8').replace(/\r\n/g, '\n');
+        const legacyGeneratedContents = [
+            legacyDefaultClaudeSettingsContent(context, context.agentDir),
+            legacyDefaultClaudeSettingsContent(context, context.profileDir)
+        ];
+        if (legacyGeneratedContents.includes(actual)) {
+            fs.rmSync(legacyPath);
+            verbose(`removed legacy generated Claude settings ${legacyPath}`);
+        }
     }
 }
 function checkRenderedProfile(projectRoot, agentDir) {
@@ -1191,6 +1191,7 @@ function checkRenderedProfile(projectRoot, agentDir) {
             rendered.context.paths.reviewDir,
             rendered.context.paths.memoriesDir,
             rendered.context.paths.codexHomeDir,
+            rendered.context.paths.liveDir,
             rendered.context.paths.overridesDir,
             rendered.context.paths.codexSkillsDir,
             rendered.context.paths.claudeSkillsDir,
@@ -1312,7 +1313,7 @@ function syncRuntimeDirs(context) {
         context.paths.codexSkillsDir,
         context.paths.claudeSkillsDir,
         context.paths.binDir,
-        path.join(context.agentDir, '.claude')
+        path.join(context.paths.liveDir, '.claude')
     ]) {
         fs.mkdirSync(dir, { recursive: true });
     }
@@ -1522,17 +1523,19 @@ function formatError(error) {
     return error instanceof Error ? error.message : String(error);
 }
 function runCodex(realBinary, permissionArgs, agentDir, configRoot, args, projectRoot, wrapperArgs) {
-    const agentsPath = path.join(agentDir, 'AGENTS.md');
+    const liveDir = profileLiveDir(agentDir);
+    const agentsPath = path.join(liveDir, 'AGENTS.md');
     if (!fs.existsSync(agentsPath)) {
         failMissingConfig('codex', agentDir);
     }
-    const guardBin = path.join(agentDir, 'bin');
-    const codexHomeDir = path.join(agentDir, 'memories', 'codex-home');
+    const guardBin = path.join(liveDir, 'bin');
+    const codexHomeDir = path.join(liveDir, 'memories', 'codex-home');
     fs.mkdirSync(codexHomeDir, { recursive: true });
     const env = {
         ...process.env,
         CODEX_HOME: codexHomeDir,
-        AGENT_DIR: agentDir,
+        AGENT_DIR: liveDir,
+        AGENT_PROFILE_DIR: agentDir,
         AGENT_RUN_PROJECT_ROOT: projectRoot,
         PATH: `${guardBin}${path.delimiter}${process.env.PATH ?? ''}`
     };
@@ -1561,16 +1564,18 @@ function buildCodexRuntimeArgs(wrapperArgs) {
     return ['-a', 'never', '-s', 'danger-full-access'];
 }
 function runClaude(realBinary, permissionArgs, agentDir, configRoot, args, projectRoot, wrapperArgs) {
-    const claudePath = path.join(agentDir, 'CLAUDE.md');
+    const liveDir = profileLiveDir(agentDir);
+    const claudePath = path.join(liveDir, 'CLAUDE.md');
     if (!fs.existsSync(claudePath)) {
         failMissingConfig('claude', agentDir);
     }
-    const guardBin = path.join(agentDir, 'bin');
-    const claudeConfigDir = path.join(agentDir, '.claude');
+    const guardBin = path.join(liveDir, 'bin');
+    const claudeConfigDir = path.join(liveDir, '.claude');
     const env = {
         ...process.env,
         CLAUDE_CONFIG_DIR: claudeConfigDir,
-        AGENT_DIR: agentDir,
+        AGENT_DIR: liveDir,
+        AGENT_PROFILE_DIR: agentDir,
         AGENT_RUN_PROJECT_ROOT: projectRoot,
         PATH: `${guardBin}${path.delimiter}${process.env.PATH ?? ''}`
     };
@@ -1581,11 +1586,14 @@ function runClaude(realBinary, permissionArgs, agentDir, configRoot, args, proje
         '--add-dir',
         projectRoot,
         '--add-dir',
-        agentDir,
+        liveDir,
         ...globalMemoryArgs(configRoot),
         ...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] : [];
@@ -2135,6 +2143,12 @@ function defaultLocalTemplate(_profile) {
         '{{ agentDir }}',
         '```',
         '',
+        'Profile source directory:',
+        '',
+        '```text',
+        '{{ profileDir }}',
+        '```',
+        '',
         'Add project-specific rules here.',
         ''
     ].join('\n');
@@ -2177,7 +2191,8 @@ function defaultNoAiFilesSnippet() {
         '## Agent File Storage',
         '',
         'Do not create AGENTS.md, CLAUDE.md, .agents, .claude, .codex, or other agent runtime files inside the project repository.',
-        'Agent-only files belong under {{ agentDir }}.',
+        'Generated agent-only files belong under {{ paths.liveDir }}.',
+        'Source config files belong under {{ profileDir }}.',
         ''
     ].join('\n');
 }
@@ -2249,8 +2264,8 @@ function defaultToolInstructionsTemplate(isClaude) {
         'Do not edit this file directly. Edit:',
         '',
         '```text',
-        '{{ agentDir }}/agent-run.jsonc',
-        '{{ agentDir }}/local.md.njk',
+        '{{ profileDir }}/agent-run.jsonc',
+        '{{ profileDir }}/local.md.njk',
         '```',
         '',
         '{% for section in renderedAgentSections %}',
@@ -2271,6 +2286,12 @@ function defaultToolInstructionsTemplate(isClaude) {
         '{{ agentDir }}',
         '```',
         '',
+        'Profile source directory:',
+        '',
+        '```text',
+        '{{ profileDir }}',
+        '```',
+        '',
         'Review directory:',
         '',
         '```text',
@@ -2310,13 +2331,14 @@ function defaultToolInstructionsTemplate(isClaude) {
         '## Tool Note',
         '',
         isClaude
-            ? 'Claude uses the generated config directory under {{ agentDir }}/.claude and may read {{ agentDir }} via `--add-dir`.'
+            ? '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.',
         '',
         '## Mandatory Path Rule',
         '',
         'Do not create AGENTS.md, CLAUDE.md, .agents, .claude, .codex, or AI-related files inside the project repository.',
-        'Agent-only files must be stored under the agent directory shown above.',
+        'Generated agent-only files must be stored under the agent directory shown above.',
+        'Source config files must be stored under the profile source directory shown above.',
         ''
     ].join('\n');
 }
@@ -2331,6 +2353,7 @@ function defaultCodexConfigTemplate() {
         'writable_roots = [',
         '  "{{ projectRoot }}",',
         '  "{{ agentDir }}",',
+        '  "{{ profileDir }}",',
         '  "{{ paths.globalMemoryDir }}"',
         ']',
         'network_access = false',
@@ -2341,6 +2364,7 @@ function defaultClaudeSettingsTemplate() {
     const envBlock = [
         '  "env": {',
         '    "AGENT_DIR": "{{ agentDir }}",',
+        '    "AGENT_PROFILE_DIR": "{{ profileDir }}",',
         '    "AGENT_RUN_PROJECT_ROOT": "{{ projectRoot }}",',
         '    "AGENT_GLOBAL_MEMORY_DIR": "{{ paths.globalMemoryDir }}"',
         '  }'
@@ -2371,6 +2395,7 @@ function defaultCodexConfigContent(context) {
         'writable_roots = [',
         `  ${jsonString(context.projectRoot)},`,
         `  ${jsonString(context.agentDir)},`,
+        `  ${jsonString(context.profileDir)},`,
         `  ${jsonString(context.paths.globalMemoryDir)}`,
         ']',
         'network_access = false',
@@ -2381,6 +2406,7 @@ function defaultClaudeSettingsContent(context) {
     const settings = {
         env: {
             AGENT_DIR: context.agentDir,
+            AGENT_PROFILE_DIR: context.profileDir,
             AGENT_RUN_PROJECT_ROOT: context.projectRoot,
             AGENT_GLOBAL_MEMORY_DIR: context.paths.globalMemoryDir
         }
@@ -2390,10 +2416,10 @@ function defaultClaudeSettingsContent(context) {
     }
     return `${JSON.stringify(settings, null, 2)}\n`;
 }
-function legacyDefaultClaudeSettingsContent(context) {
+function legacyDefaultClaudeSettingsContent(context, agentDir) {
     return `${JSON.stringify({
         env: {
-            AGENT_DIR: context.agentDir,
+            AGENT_DIR: agentDir,
             AGENT_RUN_PROJECT_ROOT: context.projectRoot,
             AGENT_GLOBAL_MEMORY_DIR: context.paths.globalMemoryDir
         }

package/examples/basic-config/agent-config/gitignore

@@ -1,21 +1,5 @@
-# Generated agent-run files
-**/AGENTS.md
-**/CLAUDE.md
-**/GEMINI.md
-**/config.toml
-
-# Generated native agent homes
-**/.agents/
-**/.claude/
-**/.codex/
-
-# Generated runtime files
-**/bin/
-**/reviews/
-**/memories/
-
-# Generated review reports
-**/REVIEW-*.md
+# Generated agent-run live profiles
+**/live/
 
 # Optional generated caches
 **/.agent-run-cache/

package/examples/basic-config/agent-config/global/snippets/no-ai-files.md.njk

@@ -7,3 +7,9 @@ Agent directory:
 ```text
 {{ agentDir }}
 ```
+
+Profile source directory:
+
+```text
+{{ profileDir }}
+```

package/examples/basic-config/agent-config/global/tool-templates/AGENTS.md.njk

@@ -10,6 +10,7 @@ Do not edit this generated file. Edit `agent-run.jsonc` and `local.md.njk`.
 
 - projectRoot: `{{ projectRoot }}`
 - agentDir: `{{ agentDir }}`
+- profileDir: `{{ profileDir }}`
 - reviewFile: `{{ paths.reviewFile }}`
 - memoriesDir: `{{ paths.memoriesDir }}`
 - globalMemoryDir: `{{ paths.globalMemoryDir }}`

package/examples/basic-config/agent-config/global/tool-templates/claude-settings.json.njk

@@ -1,6 +1,7 @@
 {% if permissionsAllow.length %}{
   "env": {
     "AGENT_DIR": "{{ agentDir }}",
+    "AGENT_PROFILE_DIR": "{{ profileDir }}",
     "AGENT_RUN_PROJECT_ROOT": "{{ projectRoot }}",
     "AGENT_GLOBAL_MEMORY_DIR": "{{ paths.globalMemoryDir }}",
     "STARTER_PROFILE": "{{ profile }}"
@@ -14,6 +15,7 @@
 {% else %}{
   "env": {
     "AGENT_DIR": "{{ agentDir }}",
+    "AGENT_PROFILE_DIR": "{{ profileDir }}",
     "AGENT_RUN_PROJECT_ROOT": "{{ projectRoot }}",
     "AGENT_GLOBAL_MEMORY_DIR": "{{ paths.globalMemoryDir }}",
     "STARTER_PROFILE": "{{ profile }}"

package/examples/basic-config/agent-config/global/tool-templates/codex-config.toml.njk

@@ -6,6 +6,7 @@ sandbox_mode = "workspace-write"
 writable_roots = [
   "{{ projectRoot }}",
   "{{ agentDir }}",
+  "{{ profileDir }}",
   "{{ paths.memoriesDir }}",
   "{{ paths.globalMemoryDir }}"
 ]

package/examples/basic-config/agent-config/starter/basic-project/local.md.njk

@@ -3,3 +3,4 @@
 This starter profile belongs to `{{ profile }}`.
 
 Use the project root at `{{ projectRoot }}` and keep generated files in `{{ agentDir }}`.
+Keep source profile edits in `{{ profileDir }}`.

package/examples/basic-config/agent-config/starter/basic-project/overrides/claude-settings.json.njk

@@ -1,6 +1,7 @@
 {% if permissionsAllow.length %}{
   "env": {
     "AGENT_DIR": "{{ agentDir }}",
+    "AGENT_PROFILE_DIR": "{{ profileDir }}",
     "AGENT_RUN_PROJECT_ROOT": "{{ projectRoot }}",
     "AGENT_GLOBAL_MEMORY_DIR": "{{ paths.globalMemoryDir }}",
     "STARTER_PROFILE": "{{ profile }}",
@@ -15,6 +16,7 @@
 {% else %}{
   "env": {
     "AGENT_DIR": "{{ agentDir }}",
+    "AGENT_PROFILE_DIR": "{{ profileDir }}",
     "AGENT_RUN_PROJECT_ROOT": "{{ projectRoot }}",
     "AGENT_GLOBAL_MEMORY_DIR": "{{ paths.globalMemoryDir }}",
     "STARTER_PROFILE": "{{ profile }}",

package/examples/basic-config/agent-config/starter/basic-project/overrides/codex-config.toml.njk

@@ -6,6 +6,7 @@ sandbox_mode = "workspace-write"
 writable_roots = [
   "{{ projectRoot }}",
   "{{ agentDir }}",
+  "{{ profileDir }}",
   "{{ paths.memoriesDir }}",
   "{{ paths.globalMemoryDir }}"
 ]

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@technomoron/agent-run",
-  "version": "0.99.12",
+  "version": "0.99.13",
   "packageManager": "pnpm@10.28.1",
   "bin": {
     "agent-run": "dist/agent-run.js"