ai-factory 2.9.3 → 2.11.0

package/README.md

@@ -72,46 +72,9 @@ Then open your AI agent and start working:
 /aif
 ```
 
-## Usage
+Need CLI flags, update/upgrade details, or extension commands? See [Getting Started](docs/getting-started.md). Need slash-command reference? See [Core Skills](docs/skills.md).
 
-If the package is installed:
-```bash
-ai-factory init
-```
-
-Or running without installation via `npx`:
-```bash
-npx ai-factory init
-```
-
-### Non-interactive mode
-
-Pass `--agents` to skip the interactive wizard:
-
-```bash
-# Agents + MCP servers
-ai-factory init --agents claude,cursor --mcp github,playwright
-
-# With specific skills
-ai-factory init --agents claude --skills commit,plan
-
-# Without base skills
-ai-factory init --agents codex --no-skills --mcp github
-```
-
-Available MCP servers: `github`, `postgres`, `filesystem`, `chrome-devtools`, `playwright`
-
-### Upgrading from v1 to v2
-
-```bash
-ai-factory upgrade
-```
-
-`ai-factory upgrade` removes old bare-named skills (`commit`, `feature`, etc.) and installs new `aif-*` prefixed versions. Custom skills are preserved.
-
-> **Note:** `ai-factory update` automatically checks npm for a newer CLI version and offers to install it before updating skills, then reports `changed/unchanged/skipped/removed` for installed base skills. Use `ai-factory update --force` for a clean reinstall of currently installed base skills.
-
-### Example Workflow
+## Example Workflow
 
 ```bash
 # Explore options and requirements before planning (optional)
@@ -144,20 +107,6 @@ ai-factory upgrade
 
 See the full [Development Workflow](docs/workflow.md) with diagram and decision table.
 
-### Auto-Generated Documentation
-
-AI Factory can generate and maintain your project docs with a single command:
-
-```bash
-/aif-docs          # Creates README + docs/ structure from your codebase
-/aif-docs --web    # Also generates a static HTML documentation site
-```
-
-- **Generates docs from scratch** — analyzes your codebase and creates a lean README + detailed `docs/` pages by topic
-- **Cleans up scattered files** — finds loose CONTRIBUTING.md, ARCHITECTURE.md, SETUP.md in your root and consolidates them into a structured `docs/` directory
-- **Keeps docs in sync** — integrates with `/aif-implement` docs policy (`Docs: yes` = mandatory docs checkpoint routed to `/aif-docs`, `Docs: no` = visible `WARN [docs]`)
-- **Builds a docs website** — `--web` generates a static HTML site with navigation and dark mode, ready to host
-
 ---
 
 ## Documentation
@@ -169,6 +118,7 @@ AI Factory can generate and maintain your project docs with a single command:
 | [Reflex Loop](docs/loop.md) | Iterative generate → evaluate → critique → refine workflow |
 | [Subagents](docs/subagents.md) | Claude Code only: repo-local planning, implementation, and loop subagents with narrow role contracts |
 | [Core Skills](docs/skills.md) | All slash commands — explore, grounded, plan, fix, implement, evolve, docs, and more |
+| [Quality Gates](docs/quality-gates.md) | Machine-readable `aif-gate-result` summaries for verify, review, security, and rules gates |
 | [Skill Evolution](docs/evolve.md) | How /aif-fix patches feed into /aif-evolve to generate smarter skill rules |
 | [Plan Files](docs/plan-files.md) | Plan files, self-improvement patches, skill acquisition |
 | [Security](docs/security.md) | Two-level security scanning for external skills |
@@ -176,22 +126,9 @@ AI Factory can generate and maintain your project docs with a single command:
 | [Configuration](docs/configuration.md) | `.ai-factory.json`, MCP servers, project structure, best practices |
 | [Config Reference](docs/config-reference.md) | Full `config.yaml` key reference and skill read/write matrix |
 
----
-
-![happy](https://github.com/ilhm344/ai-factory/blob/2.x/art/aif2.jpg)
-
-## AIF Handoff
-
-Looking for an **Autonomous Kanban board where AI agents plan, implement, and review your tasks**? Check out [aif-handoff](https://github.com/lee-to/aif-handoff) — a visual task management system built on top of AI Factory.
-
-![ui-light](https://github.com/lee-to/aif-handoff/blob/main/art/ui-light.png)
-![ui-dark](https://github.com/lee-to/aif-handoff/blob/main/art/ui-dark.png)
-![ui-light-list](https://github.com/lee-to/aif-handoff/blob/main/art/ui-light-list.png)
-![ui-dark-list](https://github.com/lee-to/aif-handoff/blob/main/art/ui-dark-list.png)
-
 ## Links
-
 - [Official Website](https://aif.cutcode.dev) - AI Factory website
+- [aif-handoff](https://github.com/lee-to/aif-handoff) - Autonomous Kanban board built on AI Factory
 - If AI Factory feels too simple for your goals, try [HLV](https://github.com/lee-to/hlv)
 - [skills.sh](https://skills.sh) - Skill marketplace
 - [Agent Skills Spec](https://agentskills.io) - Skill specification

package/dist/cli/commands/extension.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"extension.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/extension.ts"],"names":[],"mappings":"AAkDA,wBAAsB,mBAAmB,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CA6CvE;AAED,wBAAsB,sBAAsB,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CA4FxE;AAED,wBAAsB,oBAAoB,IAAI,OAAO,CAAC,IAAI,CAAC,CAoC1D;AAED,wBAAsB,sBAAsB,CAAC,IAAI,CAAC,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE;IAAE,KAAK,CAAC,EAAE,OAAO,CAAA;CAAE,GAAG,OAAO,CAAC,IAAI,CAAC,CAkFxG"}

package/dist/cli/commands/extension.js

@@ -1,18 +1,28 @@
 import chalk from 'chalk';
 import path from 'path';
-import { loadConfig, saveConfig } from '../../core/config.js';
+import { hydrateAgentFileSources, loadConfig, saveConfig } from '../../core/config.js';
+import { hydrateProjectAgentRegistry } from '../../core/agents.js';
 import { resolveExtension, removeExtensionFiles, getExtensionsDir, loadExtensionManifest, } from '../../core/extensions.js';
 import { removeExtensionMcpServers } from '../../core/mcp.js';
-import { removeSkillsForAllAgents, collectReplacedSkills, restoreBaseSkills, stripInjectionsForAllAgents, removeCustomSkillsForAllAgents, commitResolvedExtension, refreshExtensions, } from '../../core/extension-ops.js';
-export async function extensionAddCommand(source) {
-    const projectDir = process.cwd();
-    console.log(chalk.bold.blue('\n🏭 AI Factory - Install Extension\n'));
+import { collectTrackedExtensionAgentFileTargets, removeSkillsForAllAgents, collectReplacedSkills, collectManifestAgentFileTargets, removeAgentFilesForAllAgentsByTargets, removeExtensionAgentFilesForAllAgents, pruneAgentFileSources, pruneInstalledAgentFiles, pruneManagedAgentFiles, restoreBaseSkills, stripInjectionsForAllAgents, removeCustomSkillsForAllAgents, commitResolvedExtension, refreshExtensions, getManifestRuntimeIds, assertNoConfiguredRuntimeOrphans, } from '../../core/extension-ops.js';
+async function loadHydratedExtensionConfig(projectDir, options = {}) {
     const config = await loadConfig(projectDir);
     if (!config) {
         console.log(chalk.red('Error: No .ai-factory.json found.'));
-        console.log(chalk.dim('Run "ai-factory init" to set up your project first.'));
+        if (options.showInitHint) {
+            console.log(chalk.dim('Run "ai-factory init" to set up your project first.'));
+        }
         process.exit(1);
     }
+    await hydrateProjectAgentRegistry(projectDir, {
+        extensionNames: config.extensions?.map(extension => extension.name) ?? [],
+    });
+    return config;
+}
+export async function extensionAddCommand(source) {
+    const projectDir = process.cwd();
+    console.log(chalk.bold.blue('\n🏭 AI Factory - Install Extension\n'));
+    const config = await loadHydratedExtensionConfig(projectDir, { showInitHint: true });
     console.log(chalk.dim(`Installing from: ${source}\n`));
     try {
         const resolved = await resolveExtension(projectDir, source);
@@ -55,11 +65,8 @@ export async function extensionAddCommand(source) {
 export async function extensionRemoveCommand(name) {
     const projectDir = process.cwd();
     console.log(chalk.bold.blue('\n🏭 AI Factory - Remove Extension\n'));
-    const config = await loadConfig(projectDir);
-    if (!config) {
-        console.log(chalk.red('Error: No .ai-factory.json found.'));
-        process.exit(1);
-    }
+    const config = await loadHydratedExtensionConfig(projectDir);
+    await hydrateAgentFileSources(projectDir, config);
     const extensions = config.extensions ?? [];
     const index = extensions.findIndex(e => e.name === name);
     if (index < 0) {
@@ -69,6 +76,23 @@ export async function extensionRemoveCommand(name) {
     try {
         const extensionDir = path.join(getExtensionsDir(projectDir), name);
         const manifest = await loadExtensionManifest(extensionDir);
+        assertNoConfiguredRuntimeOrphans(config, getManifestRuntimeIds(manifest), name, 'remove');
+        const trackedAgentFileTargets = manifest?.agentFiles?.length
+            ? collectManifestAgentFileTargets(manifest)
+            : collectTrackedExtensionAgentFileTargets(config.agents, name);
+        if (Array.from(trackedAgentFileTargets.values()).some(targets => targets.length > 0)) {
+            const removedAgentFiles = manifest?.agentFiles?.length
+                ? await removeExtensionAgentFilesForAllAgents(projectDir, config.agents, manifest)
+                : await removeAgentFilesForAllAgentsByTargets(projectDir, config.agents, trackedAgentFileTargets);
+            pruneInstalledAgentFiles(config.agents, trackedAgentFileTargets);
+            pruneAgentFileSources(config.agents, trackedAgentFileTargets);
+            pruneManagedAgentFiles(config.agents, trackedAgentFileTargets);
+            for (const [agentId, files] of removedAgentFiles) {
+                if (files.length > 0) {
+                    console.log(chalk.green(`✓ Agent files removed for ${agentId}: ${files.join(', ')}`));
+                }
+            }
+        }
         // Strip injections before removing files
         await stripInjectionsForAllAgents(projectDir, config.agents, name, manifest);
         // Remove replacement skills (installed under base names)
@@ -119,11 +143,7 @@ export async function extensionRemoveCommand(name) {
 }
 export async function extensionListCommand() {
     const projectDir = process.cwd();
-    const config = await loadConfig(projectDir);
-    if (!config) {
-        console.log(chalk.red('Error: No .ai-factory.json found.'));
-        process.exit(1);
-    }
+    const config = await loadHydratedExtensionConfig(projectDir);
     const extensions = config.extensions ?? [];
     if (extensions.length === 0) {
         console.log(chalk.dim('\nNo extensions installed.\n'));
@@ -164,12 +184,7 @@ export async function extensionUpdateCommand(name, options) {
     if (force) {
         console.log(chalk.dim('Force mode: refreshing all extensions regardless of version\n'));
     }
-    const config = await loadConfig(projectDir);
-    if (!config) {
-        console.log(chalk.red('Error: No .ai-factory.json found.'));
-        console.log(chalk.dim('Run "ai-factory init" to set up your project first.'));
-        process.exit(1);
-    }
+    const config = await loadHydratedExtensionConfig(projectDir, { showInitHint: true });
     const extensions = config.extensions ?? [];
     if (extensions.length === 0) {
         console.log(chalk.dim('No extensions installed.\n'));

package/dist/cli/commands/extension.js.map

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package/dist/cli/commands/init.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/init.ts"],"names":[],"mappings":"AAYA,MAAM,WAAW,WAAW;IAC1B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,MAAM,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IAC1B,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AA+ED,wBAAsB,WAAW,CAAC,OAAO,GAAE,WAAgB,GAAG,OAAO,CAAC,IAAI,CAAC,CA4L1E"}
+{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/init.ts"],"names":[],"mappings":"AA4BA,MAAM,WAAW,WAAW;IAC1B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,MAAM,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IAC1B,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAuFD,wBAAsB,WAAW,CAAC,OAAO,GAAE,WAAgB,GAAG,OAAO,CAAC,IAAI,CAAC,CAgN1E"}

package/dist/cli/commands/init.js

@@ -1,14 +1,15 @@
 import chalk from 'chalk';
 import path from 'path';
 import { runWizard } from '../wizard/prompts.js';
-import { buildManagedSkillsState, buildManagedSubagentsState, installSkills, installSubagents, getAvailableSkills } from '../../core/installer.js';
+import { buildBundledAgentFileSources, buildExtensionAgentFileSources, buildManagedSkillsState, installSkills, installSubagents, getAvailableSkills, rebuildManagedAgentFilesForAgents, resolveInstalledAgentFileTargetPath, } from '../../core/installer.js';
 import { saveConfig, configExists, loadConfig, getCurrentVersion } from '../../core/config.js';
 import { configureMcp, getMcpInstructions } from '../../core/mcp.js';
-import { getAgentConfig, getAvailableAgentIds } from '../../core/agents.js';
+import { getAgentConfig, getAvailableAgentIds, hydrateProjectAgentRegistry } from '../../core/agents.js';
 import { cleanupAgentSetup, getAgentOnboarding } from '../../core/transformer.js';
 import { removeDirectory, removeFile, copyFile, fileExists, getSkillsDir } from '../../utils/fs.js';
 import { applyExtensionInjections } from '../../core/injections.js';
-import { collectReplacedSkills } from '../../core/extension-ops.js';
+import { assertNoAgentFileConflicts, collectReplacedSkills, installExtensionAgentFilesForAllAgents, mergeAgentFileSources, mergeInstalledAgentFiles, } from '../../core/extension-ops.js';
+import { loadAllExtensions } from '../../core/extensions.js';
 const VALID_MCP_KEYS = {
     github: 'mcpGithub',
     postgres: 'mcpPostgres',
@@ -67,13 +68,18 @@ function buildAnswersFromFlags(options, availableSkills) {
 async function removeAgentSetup(projectDir, agent) {
     const agentConfig = getAgentConfig(agent.id);
     await removeDirectory(path.join(projectDir, agent.skillsDir));
-    // Remove only AI Factory-managed subagents, not the entire directory.
+    // Remove only AI Factory-managed agent files, not the entire directory.
     // The directory may contain user-created custom agents unrelated to AI Factory.
-    const subagentsDir = agent.subagentsDir ?? agentConfig.subagentsDir;
-    if (subagentsDir) {
-        const managedFiles = agent.installedSubagents ?? [];
+    const agentsDir = agent.agentsDir ?? agentConfig.agentsDir;
+    if (agentsDir) {
+        const managedFiles = agent.installedAgentFiles ?? [];
         for (const relPath of managedFiles) {
-            await removeFile(path.join(projectDir, subagentsDir, relPath));
+            try {
+                await removeFile(resolveInstalledAgentFileTargetPath(projectDir, agentsDir, relPath));
+            }
+            catch (error) {
+                console.log(chalk.yellow(`Warning: Skipping unsafe managed agent file path "${relPath}" while removing ${agent.id}: ${error.message}`));
+            }
         }
     }
     await cleanupAgentSetup(agent.id, projectDir, agent.skillsDir);
@@ -84,6 +90,9 @@ export async function initCommand(options = {}) {
     console.log(chalk.bold.blue('\n🏭 AI Factory - Project Setup\n'));
     const hasExistingConfig = await configExists(projectDir);
     const existingConfig = hasExistingConfig ? await loadConfig(projectDir) : null;
+    await hydrateProjectAgentRegistry(projectDir, {
+        extensionNames: existingConfig?.extensions?.map(extension => extension.name) ?? [],
+    });
     if (hasExistingConfig) {
         console.log(chalk.yellow('Warning: .ai-factory.json already exists.'));
         console.log('Running init will reconfigure selected agents (add/remove) and reinstall base skills.\n');
@@ -118,10 +127,11 @@ export async function initCommand(options = {}) {
                 skills: answers.selectedSkills,
                 agentId: agentSelection.id,
             });
-            const installedSubagents = agentConfig.subagentsDir
+            const installedAgentFiles = agentConfig.agentsDir
                 ? await installSubagents({
                     projectDir,
-                    subagentsDir: agentConfig.subagentsDir,
+                    agentId: agentSelection.id,
+                    agentsDir: agentConfig.agentsDir,
                 })
                 : [];
             const configuredMcp = await configureMcp(projectDir, {
@@ -138,9 +148,10 @@ export async function initCommand(options = {}) {
                 id: agentSelection.id,
                 skillsDir: agentConfig.skillsDir,
                 installedSkills,
-                ...(agentConfig.subagentsDir ? {
-                    subagentsDir: agentConfig.subagentsDir,
-                    installedSubagents,
+                ...(agentConfig.agentsDir ? {
+                    agentsDir: agentConfig.agentsDir,
+                    installedAgentFiles,
+                    agentFileSources: buildBundledAgentFileSources(installedAgentFiles),
                 } : {}),
                 mcp: {
                     github: agentSelection.mcpGithub,
@@ -154,6 +165,22 @@ export async function initCommand(options = {}) {
         const existingExtensions = existingConfig?.extensions ?? [];
         // Re-apply extension injections after skill installation
         if (existingExtensions.length > 0) {
+            const loadedExtensions = await loadAllExtensions(projectDir, existingExtensions.map(extension => extension.name));
+            const conflictCheckConfig = existingConfig ?? {
+                version: getCurrentVersion(),
+                agents: installedAgents,
+                extensions: existingExtensions,
+            };
+            for (const { dir, manifest } of loadedExtensions) {
+                await assertNoAgentFileConflicts(projectDir, {
+                    ...conflictCheckConfig,
+                    extensions: existingExtensions,
+                    agents: installedAgents,
+                }, manifest);
+                const agentFileResults = await installExtensionAgentFilesForAllAgents(projectDir, installedAgents, dir, manifest);
+                mergeInstalledAgentFiles(installedAgents, agentFileResults);
+                mergeAgentFileSources(installedAgents, buildExtensionAgentFileSources(manifest));
+            }
             let totalInjections = 0;
             for (const agent of installedAgents) {
                 totalInjections += await applyExtensionInjections(projectDir, agent, existingExtensions);
@@ -166,10 +193,8 @@ export async function initCommand(options = {}) {
         for (const agent of installedAgents) {
             const managedBaseSkills = agent.installedSkills.filter(skill => !replacedSkills.has(skill));
             agent.managedSkills = await buildManagedSkillsState(projectDir, agent, managedBaseSkills);
-            if (agent.subagentsDir) {
-                agent.managedSubagents = await buildManagedSubagentsState(projectDir, agent, agent.installedSubagents ?? []);
-            }
         }
+        await rebuildManagedAgentFilesForAgents(projectDir, installedAgents);
         await saveConfig(projectDir, {
             version: getCurrentVersion(),
             agents: installedAgents,
@@ -194,9 +219,9 @@ export async function initCommand(options = {}) {
             console.log(chalk.bold(`${agentConfig.displayName}:`));
             console.log(chalk.dim(`  Skills directory: ${path.join(projectDir, agent.skillsDir)}`));
             console.log(chalk.dim(`  Installed skills: ${agent.installedSkills.length}`));
-            if (agent.subagentsDir) {
-                console.log(chalk.dim(`  Subagents directory: ${path.join(projectDir, agent.subagentsDir)}`));
-                console.log(chalk.dim(`  Installed subagents: ${agent.installedSubagents?.length ?? 0}`));
+            if (agent.agentsDir) {
+                console.log(chalk.dim(`  Agent files directory: ${path.join(projectDir, agent.agentsDir)}`));
+                console.log(chalk.dim(`  Installed agent files: ${agent.installedAgentFiles?.length ?? 0}`));
             }
             const configuredMcp = mcpSummary[agent.id];
             if (configuredMcp && configuredMcp.length > 0) {

package/dist/cli/commands/init.js.map

@@ -1 +1 @@
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package/dist/cli/commands/update.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"update.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/update.ts"],"names":[],"mappings":"AA0BA,UAAU,oBAAoB;IAC5B,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAuHD,wBAAsB,aAAa,CAAC,OAAO,GAAE,oBAAyB,GAAG,OAAO,CAAC,IAAI,CAAC,CA2SrF"}
+{"version":3,"file":"update.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/update.ts"],"names":[],"mappings":"AA+BA,UAAU,oBAAoB;IAC5B,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAyHD,wBAAsB,aAAa,CAAC,OAAO,GAAE,oBAAyB,GAAG,OAAO,CAAC,IAAI,CAAC,CAuWrF"}

package/dist/cli/commands/update.js

@@ -3,11 +3,12 @@ import path from 'path';
 import { realpathSync } from 'fs';
 import { execSync } from 'child_process';
 import inquirer from 'inquirer';
-import { getCurrentVersion, loadConfig, saveConfig } from '../../core/config.js';
-import { compareExtensionVersions, getExtensionsDir, getNpmVersionCheckResult, loadExtensionManifest } from '../../core/extensions.js';
-import { buildManagedSkillsState, buildManagedSubagentsState, getAvailableSkills, partitionSkills, updateSkills, updateSubagents, } from '../../core/installer.js';
+import { getCurrentVersion, hydrateAgentFileSources, loadConfig, saveConfig } from '../../core/config.js';
+import { compareExtensionVersions, getExtensionsDir, getNpmVersionCheckResult, loadAllExtensions } from '../../core/extensions.js';
+import { hydrateProjectAgentRegistry } from '../../core/agents.js';
+import { buildExtensionAgentFileSources, buildManagedSkillsState, getAvailableSkills, partitionSkills, rebuildManagedAgentFilesForAgents, updateSkills, updateSubagents, } from '../../core/installer.js';
 import { applyExtensionInjections } from '../../core/injections.js';
-import { installExtensionSkillsForAllAgents, installSkillsForAllAgents, collectReplacedSkills, refreshExtensions, } from '../../core/extension-ops.js';
+import { installExtensionSkillsForAllAgents, installExtensionAgentFilesForAllAgents, installSkillsForAllAgents, collectReplacedSkills, mergeAgentFileSources, mergeInstalledAgentFiles, refreshExtensions, } from '../../core/extension-ops.js';
 import { fileExists } from '../../utils/fs.js';
 function formatReason(reason) {
     switch (reason) {
@@ -33,6 +34,8 @@ function formatReason(reason) {
             return 'install failed';
         case 'source-missing':
             return 'source unavailable';
+        case 'extension-refresh':
+            return 'extension refresh';
         default:
             return reason;
     }
@@ -127,6 +130,9 @@ export async function updateCommand(options = {}) {
         console.log(chalk.dim('Run "ai-factory init" to set up your project first.'));
         process.exit(1);
     }
+    await hydrateProjectAgentRegistry(projectDir, {
+        extensionNames: config.extensions?.map(extension => extension.name) ?? [],
+    });
     const currentVersion = getCurrentVersion();
     console.log(chalk.dim(`Config version: ${config.version}`));
     console.log(chalk.dim(`Package version: ${currentVersion}\n`));
@@ -170,12 +176,22 @@ export async function updateCommand(options = {}) {
             console.log(chalk.yellow(`  ⚠ ${r.name}: ${r.failureReason}`));
         }
         console.log(chalk.dim(`Extensions: ${extensionSummary.updated.length} updated, ${extensionSummary.unchanged.length} unchanged, ${extensionSummary.failed.length} failed\n`));
+        await hydrateProjectAgentRegistry(projectDir, {
+            extensionNames: config.extensions?.map(extension => extension.name) ?? [],
+        });
     }
     console.log(chalk.dim('Updating skills and agent assets...\n'));
     try {
         const availableSkills = await getAvailableSkills();
         const skillEntriesByAgent = new Map();
         const subagentEntriesByAgent = new Map();
+        const installedExtensions = extensions.length > 0
+            ? await loadAllExtensions(projectDir, extensions.map(extension => extension.name))
+            : [];
+        const extensionManifests = new Map(installedExtensions.map(({ manifest }) => [manifest.name, manifest]));
+        await hydrateAgentFileSources(projectDir, config, {
+            installedExtensions,
+        });
         const allReplacedSkills = collectReplacedSkills(extensions);
         if (allReplacedSkills.size > 0) {
             console.log(chalk.dim(`Skipping replaced skills: ${[...allReplacedSkills].join(', ')}`));
@@ -188,7 +204,8 @@ export async function updateCommand(options = {}) {
             agent.installedSkills = result.installedSkills;
             skillEntriesByAgent.set(agent.id, result.entries);
             const subagentResult = await updateSubagents(agent, projectDir, { force });
-            agent.installedSubagents = subagentResult.installedSubagents;
+            agent.installedAgentFiles = subagentResult.installedAgentFiles;
+            agent.agentFileSources = subagentResult.agentFileSources;
             subagentEntriesByAgent.set(agent.id, subagentResult.entries);
         }
         // Re-install replacement skills from extensions
@@ -198,7 +215,7 @@ export async function updateCommand(options = {}) {
             if (!ext.replacedSkills?.length)
                 continue;
             const extensionDir = path.join(getExtensionsDir(projectDir), ext.name);
-            const manifest = await loadExtensionManifest(extensionDir);
+            const manifest = extensionManifests.get(ext.name);
             if (!manifest?.replaces) {
                 console.log(chalk.yellow(`⚠ Extension "${ext.name}" manifest missing — restoring base skills: ${ext.replacedSkills.join(', ')}`));
                 failedReplacements.push(...ext.replacedSkills);
@@ -248,6 +265,34 @@ export async function updateCommand(options = {}) {
                 await installSkillsForAllAgents(projectDir, config.agents, toRestore);
             }
         }
+        // Re-install extension-managed agent files so ordinary updates heal drift
+        // even when the extension version itself did not change.
+        for (const ext of extensions) {
+            const extensionDir = path.join(getExtensionsDir(projectDir), ext.name);
+            const manifest = extensionManifests.get(ext.name);
+            if (!manifest?.agentFiles?.length) {
+                const preservesTrackedAgentFiles = config.agents.some(agent => Object.values(agent.agentFileSources ?? {}).some(source => source.kind === 'extension' && source.extensionName === ext.name));
+                if (preservesTrackedAgentFiles) {
+                    console.log(chalk.yellow(`⚠ Extension "${ext.name}" agent file manifest missing — preserving tracked agent file state`));
+                }
+                continue;
+            }
+            const results = await installExtensionAgentFilesForAllAgents(projectDir, config.agents, extensionDir, manifest);
+            mergeInstalledAgentFiles(config.agents, results);
+            mergeAgentFileSources(config.agents, buildExtensionAgentFileSources(manifest));
+            for (const [agentId, installed] of results) {
+                if (installed.length === 0) {
+                    continue;
+                }
+                const existingEntries = subagentEntriesByAgent.get(agentId) ?? [];
+                existingEntries.push(...installed.map(subagent => ({
+                    subagent,
+                    status: 'changed',
+                    reason: 'extension-refresh',
+                })));
+                subagentEntriesByAgent.set(agentId, existingEntries);
+            }
+        }
         // Re-apply extension injections
         if (config.extensions?.length) {
             let totalInjections = 0;
@@ -264,12 +309,15 @@ export async function updateCommand(options = {}) {
             const { base: baseSkills } = partitionSkills(agent.installedSkills);
             const managedBaseSkills = baseSkills.filter(skill => availableSkills.includes(skill) && !finalReplacedSkills.has(skill));
             agent.managedSkills = await buildManagedSkillsState(projectDir, agent, managedBaseSkills);
-            if (agent.subagentsDir) {
-                agent.managedSubagents = await buildManagedSubagentsState(projectDir, agent, agent.installedSubagents ?? []);
-            }
         }
+        await rebuildManagedAgentFilesForAgents(projectDir, config.agents, {
+            preserveExistingOnMissingSource: true,
+            warn: (message) => console.log(chalk.yellow(`⚠ ${message}`)),
+        });
         config.version = currentVersion;
-        await saveConfig(projectDir, config);
+        await saveConfig(projectDir, config, {
+            installedExtensions,
+        });
         console.log(chalk.green('✓ Skills and agent assets updated successfully'));
         console.log(chalk.green('✓ Configuration updated'));
         for (const agent of config.agents) {
@@ -323,9 +371,9 @@ export async function updateCommand(options = {}) {
                 }
             }
             const subagentEntries = subagentEntriesByAgent.get(agent.id) ?? [];
-            if (agent.subagentsDir || subagentEntries.length > 0) {
+            if (agent.agentsDir || subagentEntries.length > 0) {
                 const groupedSubagents = groupAndSortEntriesByStatus(subagentEntries, e => e.subagent);
-                console.log(chalk.bold(`[${agent.id}] Subagents:`));
+                console.log(chalk.bold(`[${agent.id}] Agent files:`));
                 console.log(chalk.dim(`  changed: ${groupedSubagents.changed.length}`));
                 console.log(chalk.dim(`  unchanged: ${groupedSubagents.unchanged.length}`));
                 console.log(chalk.dim(`  skipped: ${groupedSubagents.skipped.length}`));
@@ -354,7 +402,7 @@ export async function updateCommand(options = {}) {
                     'source-missing',
                 ].includes(entry.reason));
                 if (recoveredSubagents.length > 0) {
-                    console.log(chalk.yellow('  WARN: managed subagent state recovered for:'));
+                    console.log(chalk.yellow('  WARN: managed agent file state recovered for:'));
                     for (const entry of recoveredSubagents) {
                         console.log(chalk.yellow(`    - ${entry.subagent} (${formatReason(entry.reason)})`));
                     }