ai-factory 2.1.0 → 2.2.1

package/README.md

@@ -28,11 +28,11 @@ ai-factory init
 
 ## Why AI Factory?
 
-- **Zero configuration** — detects your stack, installs relevant skills, configures integrations
+- **Zero configuration** — installs relevant skills, configures integrations
 - **Best practices built-in** — logging, commits, code review, all following industry standards
 - **Spec-driven development** — AI follows plans, not random exploration. Predictable, resumable, reviewable
 - **Community skills** — leverage [skills.sh](https://skills.sh) ecosystem or generate custom skills
-- **Works with your stack** — Next.js, Laravel, Django, Express, and more
+- **Stack-agnostic** — works with any language, framework, or platform
 - **Multi-agent support** — Claude Code, Cursor, Windsurf, Roo Code, Kilo Code, Antigravity, OpenCode, Warp, Zencoder, Codex CLI, GitHub Copilot, Gemini CLI, Junie, Qwen Code, or [any agent](docs/getting-started.md#supported-agents)
 
 ---
@@ -60,7 +60,6 @@ ai-factory init
 
 This will:
 - Ask which AI agent you use
-- Detect your project stack
 - Install relevant skills
 - Configure MCP servers (for supported agents)
 
@@ -144,6 +143,7 @@ AI Factory can generate and maintain your project docs with a single command:
 | [Core Skills](docs/skills.md) | All slash commands — feature, task, fix, implement, evolve, docs, and more |
 | [Plan Files](docs/plan-files.md) | Plan files, self-improvement patches, skill acquisition |
 | [Security](docs/security.md) | Two-level security scanning for external skills |
+| [Extensions](docs/extensions.md) | Writing and installing extensions — commands, injections, MCP, agents |
 | [Configuration](docs/configuration.md) | `.ai-factory.json`, MCP servers, project structure, best practices |
 
 ---

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

@@ -0,0 +1,4 @@
+export declare function extensionAddCommand(source: string): Promise<void>;
+export declare function extensionRemoveCommand(name: string): Promise<void>;
+export declare function extensionListCommand(): Promise<void>;
+//# sourceMappingURL=extension.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"extension.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/extension.ts"],"names":[],"mappings":"AA2BA,wBAAsB,mBAAmB,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAuKvE;AAED,wBAAsB,sBAAsB,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CA4ExE;AAED,wBAAsB,oBAAoB,IAAI,OAAO,CAAC,IAAI,CAAC,CAwC1D"}

package/dist/cli/commands/extension.js

@@ -0,0 +1,288 @@
+import chalk from 'chalk';
+import path from 'path';
+import { loadConfig, saveConfig } from '../../core/config.js';
+import { resolveExtension, commitExtensionInstall, removeExtensionFiles, getExtensionsDir, loadExtensionManifest, } from '../../core/extensions.js';
+import { applySingleExtensionInjections, } from '../../core/injections.js';
+import { configureExtensionMcpServers, removeExtensionMcpServers } from '../../core/mcp.js';
+import { installExtensionSkills } from '../../core/installer.js';
+import { readJsonFile } from '../../utils/fs.js';
+import { getAgentConfig } from '../../core/agents.js';
+import { removeSkillsForAllAgents, installExtensionSkillsForAllAgents, collectReplacedSkills, restoreBaseSkills, stripInjectionsForAllAgents, removeCustomSkillsForAllAgents, } 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'));
+    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);
+    }
+    console.log(chalk.dim(`Installing from: ${source}\n`));
+    try {
+        const extensions = config.extensions ?? [];
+        // Phase 1: Resolve source — download/clone and validate manifest WITHOUT writing to project
+        const resolved = await resolveExtension(projectDir, source);
+        const manifest = resolved.manifest;
+        try {
+            const existIdx = extensions.findIndex(e => e.name === manifest.name);
+            const oldRecord = existIdx >= 0 ? { ...extensions[existIdx] } : null;
+            // Load old manifest from installed dir (still intact — we haven't overwritten yet)
+            const oldManifest = existIdx >= 0
+                ? await loadExtensionManifest(path.join(getExtensionsDir(projectDir), manifest.name))
+                : null;
+            // Block conflicting replacements BEFORE copying any files
+            if (manifest.replaces) {
+                for (const [, baseSkillName] of Object.entries(manifest.replaces)) {
+                    for (const other of extensions) {
+                        if (other.name === manifest.name)
+                            continue;
+                        if (other.replacedSkills?.includes(baseSkillName)) {
+                            throw new Error(`Conflict: skill "${baseSkillName}" is already replaced by extension "${other.name}". Remove it first.`);
+                        }
+                    }
+                }
+            }
+            // Phase 2: Commit — copy resolved files to .ai-factory/extensions/<name>/
+            await commitExtensionInstall(projectDir, resolved);
+            // Clean up old state on re-install
+            if (existIdx >= 0) {
+                await stripInjectionsForAllAgents(projectDir, config.agents, manifest.name);
+                // Remove old replacement skills (installed under base names)
+                if (oldRecord?.replacedSkills?.length) {
+                    await removeSkillsForAllAgents(projectDir, config.agents, oldRecord.replacedSkills);
+                    await restoreBaseSkills(projectDir, config.agents, oldRecord.replacedSkills, new Set());
+                }
+                // Remove old extension custom skills using the OLD manifest (not the new one)
+                if (oldManifest) {
+                    await removeCustomSkillsForAllAgents(projectDir, config.agents, oldManifest);
+                }
+            }
+            console.log(chalk.green(`✓ Extension "${manifest.name}" v${manifest.version} installed`));
+            const extensionDir = path.join(getExtensionsDir(projectDir), manifest.name);
+            // Install replacement skills — only track successfully installed ones
+            const replacedSkills = [];
+            const replacesPaths = new Set();
+            if (manifest.replaces && Object.keys(manifest.replaces).length > 0) {
+                const nameOverrides = { ...manifest.replaces };
+                const replacePaths = Object.keys(manifest.replaces);
+                // Track per-agent success: only count as replaced if installed on ALL agents
+                const perAgentResults = new Map(); // baseName → success count
+                for (const agent of config.agents) {
+                    const installed = await installExtensionSkills(projectDir, agent, extensionDir, replacePaths, nameOverrides);
+                    for (const name of installed) {
+                        perAgentResults.set(name, (perAgentResults.get(name) ?? 0) + 1);
+                    }
+                }
+                const agentCount = config.agents.length;
+                for (const [extSkillPath, baseSkillName] of Object.entries(manifest.replaces)) {
+                    replacesPaths.add(extSkillPath);
+                    const successCount = perAgentResults.get(baseSkillName) ?? 0;
+                    if (successCount === agentCount) {
+                        replacedSkills.push(baseSkillName);
+                        console.log(chalk.green(`✓ Replaced skill "${baseSkillName}" with "${path.basename(extSkillPath)}"`));
+                    }
+                    else if (successCount > 0) {
+                        // Rollback: remove the replacement from agents where it did install, restore base skill
+                        await removeSkillsForAllAgents(projectDir, config.agents, [baseSkillName]);
+                        await restoreBaseSkills(projectDir, config.agents, [baseSkillName], new Set());
+                        console.log(chalk.yellow(`⚠ Replacement "${baseSkillName}" only installed on ${successCount}/${agentCount} agents — rolled back, base skill restored`));
+                    }
+                    else {
+                        console.log(chalk.yellow(`⚠ Failed to replace skill "${baseSkillName}" — base skill preserved`));
+                    }
+                }
+            }
+            // Install extension custom skills (excluding replacements)
+            if (manifest.skills?.length) {
+                const nonReplacementSkills = manifest.skills.filter(s => !replacesPaths.has(s));
+                if (nonReplacementSkills.length > 0) {
+                    const results = await installExtensionSkillsForAllAgents(projectDir, config.agents, extensionDir, nonReplacementSkills);
+                    for (const [agentId, installed] of results) {
+                        if (installed.length > 0) {
+                            console.log(chalk.green(`✓ Skills installed for ${agentId}: ${installed.join(', ')}`));
+                        }
+                    }
+                }
+            }
+            // Save config AFTER all installations succeed
+            const record = { name: manifest.name, source, version: manifest.version, replacedSkills: replacedSkills.length > 0 ? replacedSkills : undefined };
+            if (existIdx >= 0) {
+                extensions[existIdx] = record;
+            }
+            else {
+                extensions.push(record);
+            }
+            config.extensions = extensions;
+            await saveConfig(projectDir, config);
+            // Apply injections for all agents
+            if (manifest.injections?.length) {
+                let totalInjections = 0;
+                for (const agent of config.agents) {
+                    const count = await applySingleExtensionInjections(projectDir, agent, extensionDir, manifest);
+                    totalInjections += count;
+                }
+                if (totalInjections > 0) {
+                    console.log(chalk.green(`✓ Applied ${totalInjections} injection(s)`));
+                }
+            }
+            // Configure MCP servers for all agents that support it
+            if (manifest.mcpServers?.length) {
+                const mcpConfigured = await applyExtensionMcp(projectDir, config.agents.map(a => a.id), extensionDir, manifest);
+                if (mcpConfigured.length > 0) {
+                    console.log(chalk.green(`✓ MCP servers configured: ${mcpConfigured.join(', ')}`));
+                    for (const srv of manifest.mcpServers) {
+                        if (srv.instruction) {
+                            console.log(chalk.dim(`    ${srv.instruction}`));
+                        }
+                    }
+                }
+            }
+            if (manifest.agents?.length) {
+                console.log(chalk.dim(`  Agents provided: ${manifest.agents.map(a => a.displayName).join(', ')}`));
+            }
+            if (manifest.commands?.length) {
+                console.log(chalk.dim(`  Commands provided: ${manifest.commands.map(c => c.name).join(', ')}`));
+            }
+            if (manifest.skills?.length) {
+                console.log(chalk.dim(`  Skills provided: ${manifest.skills.join(', ')}`));
+            }
+            console.log('');
+        }
+        finally {
+            await resolved.cleanup();
+        }
+    }
+    catch (error) {
+        console.log(chalk.red(`Error installing extension: ${error.message}`));
+        process.exit(1);
+    }
+}
+export async function extensionRemoveCommand(name) {
+    const projectDir = process.cwd();
+    console.log(chalk.bold.blue('\n🏭 AI Factory - Remove Extension\n'));
+    const config = await loadConfig(projectDir);
+    if (!config) {
+        console.log(chalk.red('Error: No .ai-factory.json found.'));
+        process.exit(1);
+    }
+    const extensions = config.extensions ?? [];
+    const index = extensions.findIndex(e => e.name === name);
+    if (index < 0) {
+        console.log(chalk.red(`Extension "${name}" is not installed.`));
+        process.exit(1);
+    }
+    try {
+        const extensionDir = path.join(getExtensionsDir(projectDir), name);
+        const manifest = await loadExtensionManifest(extensionDir);
+        // Strip injections before removing files
+        await stripInjectionsForAllAgents(projectDir, config.agents, name, manifest);
+        // Remove replacement skills (installed under base names)
+        const extRecord = extensions[index];
+        if (extRecord.replacedSkills?.length) {
+            const removed = await removeSkillsForAllAgents(projectDir, config.agents, extRecord.replacedSkills);
+            for (const [agentId, skills] of removed) {
+                if (skills.length > 0) {
+                    console.log(chalk.green(`✓ Replacement skills removed for ${agentId}: ${skills.join(', ')}`));
+                }
+            }
+        }
+        // Remove extension custom skills
+        if (manifest) {
+            const removed = await removeCustomSkillsForAllAgents(projectDir, config.agents, manifest);
+            for (const [agentId, skills] of removed) {
+                if (skills.length > 0) {
+                    console.log(chalk.green(`✓ Skills removed for ${agentId}: ${skills.join(', ')}`));
+                }
+            }
+        }
+        // Restore base skills if no other extension replaces them
+        if (extRecord.replacedSkills?.length) {
+            const stillReplaced = collectReplacedSkills(extensions, name);
+            const restored = await restoreBaseSkills(projectDir, config.agents, extRecord.replacedSkills, stillReplaced);
+            if (restored.length > 0) {
+                console.log(chalk.green(`✓ Restored base skills: ${restored.join(', ')}`));
+            }
+        }
+        // Remove MCP servers
+        if (manifest?.mcpServers?.length) {
+            const mcpKeys = manifest.mcpServers.map(s => s.key);
+            for (const agent of config.agents) {
+                await removeExtensionMcpServers(projectDir, agent.id, mcpKeys);
+            }
+        }
+        await removeExtensionFiles(projectDir, name);
+        extensions.splice(index, 1);
+        config.extensions = extensions;
+        await saveConfig(projectDir, config);
+        console.log(chalk.green(`✓ Extension "${name}" removed`));
+        console.log('');
+    }
+    catch (error) {
+        console.log(chalk.red(`Error removing extension: ${error.message}`));
+        process.exit(1);
+    }
+}
+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 extensions = config.extensions ?? [];
+    if (extensions.length === 0) {
+        console.log(chalk.dim('\nNo extensions installed.\n'));
+        return;
+    }
+    console.log(chalk.bold('\nInstalled extensions:\n'));
+    for (const ext of extensions) {
+        console.log(`  ${chalk.bold(ext.name)} ${chalk.dim(`v${ext.version}`)}`);
+        console.log(chalk.dim(`    Source: ${ext.source}`));
+        const extensionDir = path.join(getExtensionsDir(projectDir), ext.name);
+        const manifest = await loadExtensionManifest(extensionDir);
+        if (manifest) {
+            if (manifest.description) {
+                console.log(chalk.dim(`    ${manifest.description}`));
+            }
+            const features = [];
+            if (manifest.commands?.length)
+                features.push(`${manifest.commands.length} command(s)`);
+            if (manifest.agents?.length)
+                features.push(`${manifest.agents.length} agent(s)`);
+            if (manifest.injections?.length)
+                features.push(`${manifest.injections.length} injection(s)`);
+            if (manifest.skills?.length)
+                features.push(`${manifest.skills.length} skill(s)`);
+            if (manifest.mcpServers?.length)
+                features.push(`${manifest.mcpServers.length} MCP server(s)`);
+            if (features.length > 0) {
+                console.log(chalk.dim(`    Provides: ${features.join(', ')}`));
+            }
+        }
+    }
+    console.log('');
+}
+async function applyExtensionMcp(projectDir, agentIds, extensionDir, manifest) {
+    if (!manifest.mcpServers?.length)
+        return [];
+    const allConfigured = [];
+    for (const srv of manifest.mcpServers) {
+        const templatePath = path.join(extensionDir, srv.template);
+        const template = await readJsonFile(templatePath);
+        if (!template)
+            continue;
+        for (const agentId of agentIds) {
+            const agentConfig = getAgentConfig(agentId);
+            if (!agentConfig.supportsMcp)
+                continue;
+            const configured = await configureExtensionMcpServers(projectDir, agentId, [
+                { key: srv.key, template },
+            ]);
+            if (configured.length > 0 && !allConfigured.includes(srv.key)) {
+                allConfigured.push(srv.key);
+            }
+        }
+    }
+    return allConfigured;
+}
+//# sourceMappingURL=extension.js.map

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

@@ -0,0 +1 @@
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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":"AAqCA,wBAAsB,WAAW,IAAI,OAAO,CAAC,IAAI,CAAC,CAiIjD"}
+{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/init.ts"],"names":[],"mappings":"AAgBA,wBAAsB,WAAW,IAAI,OAAO,CAAC,IAAI,CAAC,CA4IjD"}

package/dist/cli/commands/init.js

@@ -5,29 +5,12 @@ import { installSkills } from '../../core/installer.js';
 import { saveConfig, configExists, loadConfig, getCurrentVersion } from '../../core/config.js';
 import { configureMcp, getMcpInstructions } from '../../core/mcp.js';
 import { getAgentConfig } from '../../core/agents.js';
-import { getTransformer } from '../../core/transformer.js';
-import { WORKFLOW_SKILLS } from '../../core/transformer.js';
-import { fileExists, removeDirectory, removeFile } from '../../utils/fs.js';
+import { cleanupAgentSetup, getAgentOnboarding } from '../../core/transformer.js';
+import { removeDirectory } from '../../utils/fs.js';
+import { applyExtensionInjections } from '../../core/injections.js';
 async function removeAgentSetup(projectDir, agent) {
-    const agentConfig = getAgentConfig(agent.id);
     await removeDirectory(path.join(projectDir, agent.skillsDir));
-    if (agent.id === 'antigravity') {
-        const workflowsDir = path.join(projectDir, agentConfig.configDir, 'workflows');
-        for (const workflow of WORKFLOW_SKILLS) {
-            const workflowFile = path.join(workflowsDir, `${workflow}.md`);
-            if (await fileExists(workflowFile)) {
-                await removeFile(workflowFile);
-            }
-        }
-        for (const ruleFile of ['aif-guardrails.md', 'aif-conventions.md']) {
-            const rulePath = path.join(projectDir, agentConfig.configDir, 'rules', ruleFile);
-            if (await fileExists(rulePath)) {
-                await removeFile(rulePath);
-            }
-        }
-    }
-    // Keep agent settings file intact: it may contain user-managed configuration
-    // unrelated to AI Factory.
+    await cleanupAgentSetup(agent.id, projectDir, agent.skillsDir);
 }
 export async function initCommand() {
     const projectDir = process.cwd();
@@ -40,7 +23,7 @@ export async function initCommand() {
     }
     try {
         const existingAgentIds = existingConfig?.agents.map(agent => agent.id) ?? [];
-        const answers = await runWizard(projectDir, existingAgentIds);
+        const answers = await runWizard(existingAgentIds);
         const selectedAgentIds = new Set(answers.agents.map(agent => agent.id));
         const removedAgents = (existingConfig?.agents ?? []).filter(agent => !selectedAgentIds.has(agent.id));
         if (removedAgents.length > 0) {
@@ -59,7 +42,6 @@ export async function initCommand() {
                 projectDir,
                 skillsDir: agentConfig.skillsDir,
                 skills: answers.selectedSkills,
-                stack: null, // Stack-specific skills generated by /aif in Claude
                 agentId: agentSelection.id,
             });
             const configuredMcp = await configureMcp(projectDir, {
@@ -67,6 +49,7 @@ export async function initCommand() {
                 filesystem: agentSelection.mcpFilesystem,
                 postgres: agentSelection.mcpPostgres,
                 chromeDevtools: agentSelection.mcpChromeDevtools,
+                playwright: agentSelection.mcpPlaywright,
             }, agentSelection.id);
             if (configuredMcp.length > 0) {
                 mcpSummary[agentSelection.id] = configuredMcp;
@@ -80,13 +63,26 @@ export async function initCommand() {
                     filesystem: agentSelection.mcpFilesystem,
                     postgres: agentSelection.mcpPostgres,
                     chromeDevtools: agentSelection.mcpChromeDevtools,
+                    playwright: agentSelection.mcpPlaywright,
                 },
             });
         }
+        const existingExtensions = existingConfig?.extensions ?? [];
         await saveConfig(projectDir, {
             version: getCurrentVersion(),
             agents: installedAgents,
+            extensions: existingExtensions,
         });
+        // Re-apply extension injections after skill installation
+        if (existingExtensions.length > 0) {
+            let totalInjections = 0;
+            for (const agent of installedAgents) {
+                totalInjections += await applyExtensionInjections(projectDir, agent, existingExtensions);
+            }
+            if (totalInjections > 0) {
+                console.log(chalk.green(`✓ Re-applied ${totalInjections} extension injection(s)`));
+            }
+        }
         console.log(chalk.green('✓ Configuration saved to .ai-factory.json'));
         console.log(chalk.bold.green('\n✅ Setup complete!\n'));
         for (const agent of installedAgents) {
@@ -105,27 +101,21 @@ export async function initCommand() {
             console.log('');
         }
         console.log(chalk.bold('\nNext steps:'));
-        const includesCodex = installedAgents.some(agent => agent.id === 'codex');
-        const includesQwen = installedAgents.some(agent => agent.id === 'qwen');
-        for (const [index, agent] of installedAgents.entries()) {
+        const onboardingByAgent = installedAgents.map(agent => ({
+            agent,
+            onboarding: getAgentOnboarding(agent.id),
+        }));
+        for (const [index, { agent, onboarding }] of onboardingByAgent.entries()) {
             const agentConfig = getAgentConfig(agent.id);
-            const transformer = getTransformer(agent.id);
-            const welcomeMessage = transformer.getWelcomeMessage?.();
             console.log(chalk.dim(`  ${index + 1}. ${agentConfig.displayName}`));
-            if (welcomeMessage) {
-                for (const line of welcomeMessage) {
-                    console.log(chalk.dim(`     ${line}`));
-                }
-            }
-            else {
-                console.log(chalk.dim('     Open the agent in this directory'));
-                console.log(chalk.dim('     Run /aif to analyze project and generate stack-specific skills'));
+            for (const line of onboarding.welcomeMessage) {
+                console.log(chalk.dim(`     ${line}`));
             }
         }
-        const invocationHints = [
-            includesCodex ? 'Codex CLI: $aif-plan, $aif-commit' : null,
-            includesQwen ? 'Qwen Code: /skills aif-plan, /skills aif-commit' : null,
-        ].filter(Boolean).join('; ');
+        const invocationHints = onboardingByAgent
+            .map(({ onboarding }) => onboarding.invocationHint)
+            .filter(Boolean)
+            .join('; ');
         console.log(chalk.dim(`  ${installedAgents.length + 1}. Use /aif-plan and /aif-commit for daily workflow${invocationHints ? ` (${invocationHints})` : ''}`));
         console.log('');
     }

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":"AAIA,wBAAsB,aAAa,IAAI,OAAO,CAAC,IAAI,CAAC,CAwEnD"}
+{"version":3,"file":"update.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/update.ts"],"names":[],"mappings":"AAYA,wBAAsB,aAAa,IAAI,OAAO,CAAC,IAAI,CAAC,CA0JnD"}

package/dist/cli/commands/update.js

@@ -1,6 +1,10 @@
 import chalk from 'chalk';
-import { loadConfig, saveConfig, getCurrentVersion } from '../../core/config.js';
-import { updateSkills, getAvailableSkills } from '../../core/installer.js';
+import path from 'path';
+import { getCurrentVersion, loadConfig, saveConfig } from '../../core/config.js';
+import { getAvailableSkills, partitionSkills, updateSkills } from '../../core/installer.js';
+import { applyExtensionInjections } from '../../core/injections.js';
+import { getExtensionsDir, loadExtensionManifest } from '../../core/extensions.js';
+import { installExtensionSkillsForAllAgents, installSkillsForAllAgents, collectReplacedSkills, } from '../../core/extension-ops.js';
 export async function updateCommand() {
     const projectDir = process.cwd();
     console.log(chalk.bold.blue('\n🏭 AI Factory - Update Skills\n'));
@@ -18,19 +22,95 @@ export async function updateCommand() {
         const availableSkills = await getAvailableSkills();
         const previousBaseSkillsByAgent = new Map();
         for (const agent of config.agents) {
-            const previousBaseSkills = agent.installedSkills.filter(s => !s.includes('/'));
+            const { base: previousBaseSkills } = partitionSkills(agent.installedSkills);
             previousBaseSkillsByAgent.set(agent.id, previousBaseSkills);
             const newSkills = availableSkills.filter(s => !previousBaseSkills.includes(s));
+            const removedSkills = previousBaseSkills.filter(s => !availableSkills.includes(s));
             if (newSkills.length > 0) {
                 console.log(chalk.cyan(`📦 [${agent.id}] New skills available: ${newSkills.join(', ')}`));
             }
+            if (removedSkills.length > 0) {
+                console.log(chalk.yellow(`🗑️  [${agent.id}] Removed skills: ${removedSkills.join(', ')}`));
+            }
         }
         if (config.agents.length > 0) {
             console.log('');
         }
+        // Collect all replaced skills from extensions
+        const extensions = config.extensions ?? [];
+        const allReplacedSkills = collectReplacedSkills(extensions);
+        if (allReplacedSkills.size > 0) {
+            console.log(chalk.dim(`Skipping replaced skills: ${[...allReplacedSkills].join(', ')}`));
+        }
         for (const agent of config.agents) {
-            const updatedSkills = await updateSkills(agent, projectDir);
-            agent.installedSkills = updatedSkills;
+            agent.installedSkills = await updateSkills(agent, projectDir, [...allReplacedSkills]);
+        }
+        // Re-install replacement skills from extensions
+        // Fix 3: If manifest fails to load, fall back to installing the base skill
+        const failedReplacements = [];
+        for (const ext of extensions) {
+            if (!ext.replacedSkills?.length)
+                continue;
+            const extensionDir = path.join(getExtensionsDir(projectDir), ext.name);
+            const manifest = await loadExtensionManifest(extensionDir);
+            if (!manifest?.replaces) {
+                console.log(chalk.yellow(`⚠ Extension "${ext.name}" manifest missing — restoring base skills: ${ext.replacedSkills.join(', ')}`));
+                failedReplacements.push(...ext.replacedSkills);
+                ext.replacedSkills = [];
+                continue;
+            }
+            const nameOverrides = { ...manifest.replaces };
+            const manifestBaseSkills = new Set(Object.values(manifest.replaces));
+            const replacePaths = Object.entries(manifest.replaces)
+                .filter(([, baseSkill]) => ext.replacedSkills.includes(baseSkill))
+                .map(([extPath]) => extPath);
+            // Detect replacedSkills in config that no longer exist in manifest.replaces
+            const orphanedReplacements = ext.replacedSkills.filter(s => !manifestBaseSkills.has(s));
+            if (orphanedReplacements.length > 0) {
+                console.log(chalk.yellow(`⚠ Extension "${ext.name}" no longer replaces: ${orphanedReplacements.join(', ')}`));
+                failedReplacements.push(...orphanedReplacements);
+                ext.replacedSkills = ext.replacedSkills.filter(s => manifestBaseSkills.has(s));
+            }
+            if (replacePaths.length > 0) {
+                const results = await installExtensionSkillsForAllAgents(projectDir, config.agents, extensionDir, replacePaths, nameOverrides);
+                // Detect replacements that failed to install on all agents
+                const agentCount = config.agents.length;
+                for (const [extPath, baseSkill] of Object.entries(manifest.replaces)) {
+                    if (!ext.replacedSkills.includes(baseSkill))
+                        continue;
+                    if (!replacePaths.includes(extPath))
+                        continue;
+                    let successCount = 0;
+                    for (const installed of results.values()) {
+                        if (installed.includes(baseSkill))
+                            successCount++;
+                    }
+                    if (successCount < agentCount) {
+                        console.log(chalk.yellow(`⚠ Extension "${ext.name}" replacement "${baseSkill}" failed to install — restoring base skill`));
+                        failedReplacements.push(baseSkill);
+                        ext.replacedSkills = ext.replacedSkills.filter(s => s !== baseSkill);
+                    }
+                }
+            }
+        }
+        // Install base skills that couldn't be replaced due to broken extensions
+        // But only if no other extension still replaces them
+        if (failedReplacements.length > 0) {
+            const stillReplacedByOthers = collectReplacedSkills(extensions);
+            const toRestore = failedReplacements.filter(s => !stillReplacedByOthers.has(s));
+            if (toRestore.length > 0) {
+                await installSkillsForAllAgents(projectDir, config.agents, toRestore);
+            }
+        }
+        // Re-apply extension injections
+        if (config.extensions?.length) {
+            let totalInjections = 0;
+            for (const agent of config.agents) {
+                totalInjections += await applyExtensionInjections(projectDir, agent, config.extensions);
+            }
+            if (totalInjections > 0) {
+                console.log(chalk.green(`✓ Re-applied ${totalInjections} extension injection(s)`));
+            }
         }
         config.version = currentVersion;
         await saveConfig(projectDir, config);
@@ -39,8 +119,7 @@ export async function updateCommand() {
         for (const agent of config.agents) {
             const previousBaseSkills = previousBaseSkillsByAgent.get(agent.id) ?? [];
             const newSkills = availableSkills.filter(s => !previousBaseSkills.includes(s));
-            const baseSkills = agent.installedSkills.filter(s => !s.includes('/'));
-            const customSkills = agent.installedSkills.filter(s => s.includes('/'));
+            const { base: baseSkills, custom: customSkills } = partitionSkills(agent.installedSkills);
             console.log(chalk.bold(`\n[${agent.id}] Base skills:`));
             for (const skill of baseSkills) {
                 const isNew = newSkills.includes(skill);