@bradtaylorsf/alpha-loop 1.0.1 → 1.1.0

package/dist/cli.js

@@ -1,21 +1,21 @@
 #!/usr/bin/env node
 import { program } from 'commander';
-import { initCommand } from './commands/init.js';
 import { historyCommand } from './commands/history.js';
 import { scanCommand } from './commands/scan.js';
 import { visionCommand } from './commands/vision.js';
 import { authCommand } from './commands/auth.js';
-import { syncCommand, migrateToTemplates, syncAgentAssets } from './commands/sync.js';
-import { loadConfig } from './lib/config.js';
-import { log } from './lib/logger.js';
+import { syncCommand } from './commands/sync.js';
 program
     .name('alpha-loop')
     .description('Agent-agnostic automated development loop')
-    .version('1.0.1');
+    .version('1.1.0');
 program
     .command('init')
-    .description('Create .alpha-loop.yaml config template')
-    .action(initCommand);
+    .description('Full project onboarding: config, templates, vision, scan, sync')
+    .action(async () => {
+    const { initCommand } = await import('./commands/init.js');
+    await initCommand();
+});
 program
     .command('run')
     .description('Run the loop — fetches matching issues and processes them all, then exits')
@@ -55,19 +55,6 @@ program
     .description('Sync .alpha-loop/templates/ to all configured harnesses')
     .option('--check', 'Check for drift without syncing (exits non-zero if drift found)')
     .action(syncCommand);
-program
-    .command('migrate')
-    .description('Migrate legacy skills/, AGENTS.md, .claude/agents/ into .alpha-loop/templates/')
-    .action(() => {
-    migrateToTemplates();
-    const config = loadConfig();
-    if (config.harnesses.length > 0) {
-        const result = syncAgentAssets(config.harnesses);
-        if (result.synced) {
-            log.success('Synced templates to configured harnesses');
-        }
-    }
-});
 program
     .command('resume')
     .description('Resume stranded work — push branches, run review, open PRs')

package/dist/cli.js.map

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package/dist/commands/init.d.ts

@@ -1 +1 @@
-export declare function initCommand(): void;
+export declare function initCommand(): Promise<void>;

package/dist/commands/init.js

@@ -1,38 +1,25 @@
-import { existsSync, writeFileSync, readFileSync, mkdirSync, realpathSync } from 'node:fs';
-import { join, dirname } from 'node:path';
-import { detectRepo, loadConfig } from '../lib/config.js';
-import { exec } from '../lib/shell.js';
-import { log } from '../lib/logger.js';
-import { syncAgentAssets } from './sync.js';
 /**
- * Find the templates directory shipped with alpha-loop.
- * Works whether running from src/ (tsx) or dist/ (compiled) or as an npm package.
+ * Init Command — full project onboarding for alpha-loop.
  *
- * Uses the resolved path of the CLI entrypoint (process.argv[1]) to locate the
- * package root, following symlinks so globally-installed npm packages resolve correctly.
+ * Steps:
+ * 1. Create config (.alpha-loop.yaml)
+ * 2. Set up .gitignore
+ * 3. Detect and migrate legacy layout (skills/ at root, .claude/agents/)
+ * 4. Seed .alpha-loop/templates/ from distribution (fills gaps only)
+ * 5. Install playwright-cli skills (if available)
+ * 6. Run vision (interactive, if TTY)
+ * 7. Run scan (generates context + instructions)
+ * 8. Sync templates to configured harnesses
+ * 9. Install GitHub issue template
+ * 10. Commit generated files
  */
-function findTemplatesDir() {
-    // Resolve symlinks (npm global installs are symlinked from bin/ to the actual package)
-    let startDir;
-    try {
-        startDir = dirname(realpathSync(process.argv[1]));
-    }
-    catch {
-        startDir = process.cwd();
-    }
-    // Walk up from the entrypoint to find templates/
-    let dir = startDir;
-    for (let i = 0; i < 5; i++) {
-        const candidate = join(dir, 'templates');
-        if (existsSync(candidate))
-            return candidate;
-        const parent = dirname(dir);
-        if (parent === dir)
-            break;
-        dir = parent;
-    }
-    return null;
-}
+import { existsSync, writeFileSync, readFileSync, readdirSync, copyFileSync, mkdirSync } from 'node:fs';
+import { join } from 'node:path';
+import { detectRepo, loadConfig } from '../lib/config.js';
+import { exec } from '../lib/shell.js';
+import { log } from '../lib/logger.js';
+import { syncAgentAssets, migrateToTemplates } from './sync.js';
+import { findDistributionTemplatesDir } from '../lib/templates.js';
 const CONFIG_FILE = '.alpha-loop.yaml';
 const ISSUE_TEMPLATE = `name: Agent-Ready Task
 description: A well-structured task for the automated agent loop to implement
@@ -115,8 +102,7 @@ dev_command: pnpm dev
 port: 3000
 auto_merge: true
 
-# Coding harnesses to sync skills/agents to (run 'alpha-loop sync' after changes)
-# See full list: https://github.com/nicepkg/playwright-cli
+# Coding harnesses to sync skills/agents to
 harnesses:
   - claude-code
   - codex
@@ -126,9 +112,6 @@ max_issues: 20
 max_session_duration: 7200  # 2 hours in seconds
 `;
 }
-/**
- * Copy a directory recursively using the shell (simple and reliable).
- */
 function copyDir(src, dest) {
     mkdirSync(dest, { recursive: true });
     exec(`cp -R "${src}/"* "${dest}/" 2>/dev/null || true`);
@@ -137,12 +120,9 @@ const GITIGNORE_ENTRIES = [
     '# Alpha-loop ephemeral data (not shared)',
     '.alpha-loop/sessions/',
     '.alpha-loop/auth/',
+    '.alpha-loop/templates/*.bak',
     '.worktrees/',
 ];
-/**
- * Ensure .gitignore tracks learnings but ignores sessions, auth, and worktrees.
- * Also removes stale entries that previously ignored learnings.
- */
 function ensureGitignore() {
     const gitignorePath = '.gitignore';
     let content = existsSync(gitignorePath) ? readFileSync(gitignorePath, 'utf-8') : '';
@@ -156,7 +136,6 @@ function ensureGitignore() {
         changed = true;
         log.info('Removed .alpha-loop/learnings/ from .gitignore (learnings are now tracked)');
     }
-    // Add required ignore entries
     const missing = GITIGNORE_ENTRIES.filter((entry) => !content.includes(entry));
     if (missing.length > 0) {
         const suffix = (content.endsWith('\n') || content === '') ? '' : '\n';
@@ -168,10 +147,12 @@ function ensureGitignore() {
         log.success('Updated .gitignore for alpha-loop');
     }
 }
-export function initCommand() {
-    // Create config if it doesn't exist
+export async function initCommand() {
+    const projectDir = process.cwd();
+    // --- Step 1: Create config ---
+    log.step('Step 1: Configuration');
     if (existsSync(CONFIG_FILE)) {
-        log.info(`${CONFIG_FILE} already exists — skipping config creation`);
+        log.info(`${CONFIG_FILE} already exists — skipping`);
     }
     else {
         let repo = detectRepo();
@@ -185,27 +166,70 @@ export function initCommand() {
         writeFileSync(CONFIG_FILE, configTemplate(repo));
         log.success(`Created ${CONFIG_FILE}`);
     }
-    // Everything below is idempotent — safe to re-run
-    // Ensure .gitignore has the right alpha-loop entries:
-    // - Track learnings (team-shared knowledge)
-    // - Ignore sessions (local logs, screenshots, ephemeral data)
-    // - Ignore auth (browser state with credentials)
+    // --- Step 2: Set up .gitignore ---
+    log.step('Step 2: Git ignore');
     ensureGitignore();
-    // Install playwright-cli skills if playwright-cli is available
+    // --- Step 3: Detect and migrate legacy layout (before seeding, to preserve user skills) ---
+    log.step('Step 3: Legacy migration');
+    migrateToTemplates(projectDir);
+    // --- Step 4: Seed .alpha-loop/templates/ from distribution (only fills gaps) ---
+    log.step('Step 4: Seed templates');
+    const distTemplatesDir = findDistributionTemplatesDir();
+    const projectTemplatesDir = join(projectDir, '.alpha-loop', 'templates');
+    if (distTemplatesDir) {
+        // Seed skills
+        const distSkills = join(distTemplatesDir, 'skills');
+        const projectSkills = join(projectTemplatesDir, 'skills');
+        if (existsSync(distSkills)) {
+            const skillNames = readdirSync(distSkills, { withFileTypes: true })
+                .filter((d) => d.isDirectory()).map((d) => d.name);
+            let installed = 0;
+            for (const name of skillNames) {
+                const dest = join(projectSkills, name);
+                if (!existsSync(dest)) {
+                    copyDir(join(distSkills, name), dest);
+                    installed++;
+                }
+            }
+            if (installed > 0) {
+                log.success(`Seeded ${installed} skill(s) to .alpha-loop/templates/skills/`);
+            }
+        }
+        // Seed agents
+        const distAgents = join(distTemplatesDir, 'agents');
+        const projectAgents = join(projectTemplatesDir, 'agents');
+        if (existsSync(distAgents)) {
+            mkdirSync(projectAgents, { recursive: true });
+            const agentFiles = readdirSync(distAgents).filter((f) => f.endsWith('.md'));
+            let installed = 0;
+            for (const file of agentFiles) {
+                const dest = join(projectAgents, file);
+                if (!existsSync(dest)) {
+                    copyFileSync(join(distAgents, file), dest);
+                    installed++;
+                }
+            }
+            if (installed > 0) {
+                log.success(`Seeded ${installed} agent(s) to .alpha-loop/templates/agents/`);
+            }
+        }
+    }
+    else {
+        log.warn('Distribution templates not found — skipping seed');
+    }
+    // --- Step 5: Install playwright-cli skills ---
+    log.step('Step 5: Playwright CLI');
     const which = exec('which playwright-cli');
     if (which.exitCode === 0) {
-        log.info('Installing playwright-cli skills...');
         const result = exec('playwright-cli install --skills');
         if (result.exitCode === 0) {
             log.success('Playwright CLI skills installed');
-            // playwright-cli installs to .claude/skills/ only.
-            // Copy to skills/ (source of truth) so our sync propagates to .agents/skills/ too.
+            // Copy to templates source of truth
             const installed = join('.claude', 'skills', 'playwright-cli');
-            const sourceOfTruth = join('skills', 'playwright-cli');
-            if (existsSync(installed) && !existsSync(sourceOfTruth)) {
-                mkdirSync('skills', { recursive: true });
-                copyDir(installed, sourceOfTruth);
-                log.info('Copied playwright-cli skill to skills/ (source of truth)');
+            const dest = join(projectTemplatesDir, 'skills', 'playwright-cli');
+            if (existsSync(installed) && !existsSync(dest)) {
+                copyDir(installed, dest);
+                log.info('Copied playwright-cli skill to .alpha-loop/templates/skills/');
             }
         }
         else {
@@ -213,70 +237,61 @@ export function initCommand() {
         }
     }
     else {
-        log.info('playwright-cli not found — skipping skill install. Install with: npm install -g @playwright/cli@latest');
+        log.info('playwright-cli not found — skipping. Install with: npm install -g @playwright/cli@latest');
     }
-    // Install base skills and agents from alpha-loop's templates
-    // These are the universal skills every project needs for the loop to work well
-    const templatesDir = findTemplatesDir();
-    if (templatesDir) {
-        // Install skills to skills/ (source of truth)
-        const templateSkills = join(templatesDir, 'skills');
-        if (existsSync(templateSkills)) {
-            const skillNames = exec(`ls "${templateSkills}"`).stdout.trim().split('\n').filter(Boolean);
-            let installed = 0;
-            for (const name of skillNames) {
-                const dest = join('skills', name);
-                if (!existsSync(dest)) {
-                    mkdirSync('skills', { recursive: true });
-                    copyDir(join(templateSkills, name), dest);
-                    installed++;
-                }
-            }
-            if (installed > 0) {
-                log.success(`Installed ${installed} base skill(s): ${skillNames.filter(n => !existsSync(join('skills', n)) || installed > 0).join(', ')}`);
-            }
+    // --- Step 6: Vision (interactive) ---
+    if (process.stdin.isTTY) {
+        const { hasVision } = await import('../lib/vision.js');
+        if (!hasVision()) {
+            log.step('Step 6: Project vision');
+            const { visionCommand } = await import('./vision.js');
+            await visionCommand();
         }
-        // Install agents to agents/ (will be synced by AGENTS.md convention)
-        // Also install directly to .claude/agents/ and .codex/agents/ for immediate use
-        const templateAgents = join(templatesDir, 'agents');
-        if (existsSync(templateAgents)) {
-            const agentFiles = exec(`ls "${templateAgents}"`).stdout.trim().split('\n').filter(Boolean);
-            for (const file of agentFiles) {
-                // .claude/agents/ for Claude
-                const claudeDest = join('.claude', 'agents', file);
-                if (!existsSync(claudeDest)) {
-                    mkdirSync(join('.claude', 'agents'), { recursive: true });
-                    exec(`cp "${join(templateAgents, file)}" "${claudeDest}"`);
-                }
-                // .codex/agents/ for Codex (TOML format would be different, but .md works as fallback)
-                const codexDest = join('.codex', 'agents', file);
-                if (!existsSync(codexDest)) {
-                    mkdirSync(join('.codex', 'agents'), { recursive: true });
-                    exec(`cp "${join(templateAgents, file)}" "${codexDest}"`);
-                }
-            }
-            log.success(`Installed agent definitions: ${agentFiles.join(', ')}`);
+        else {
+            log.step('Step 6: Project vision (already exists)');
         }
     }
     else {
-        log.warn('Templates directory not found — skipping base skills/agents install');
+        log.step('Step 6: Project vision (skipped — non-interactive)');
+    }
+    // --- Step 7: Scan (context + instructions) ---
+    log.step('Step 7: Scan codebase');
+    const { scanCommand } = await import('./scan.js');
+    scanCommand();
+    // --- Step 8: Sync to harnesses ---
+    log.step('Step 8: Sync to harnesses');
+    const config = loadConfig();
+    const harnesses = config.harnesses.length > 0 ? config.harnesses : ['claude-code', 'codex'];
+    const syncResult = syncAgentAssets(harnesses);
+    if (syncResult.synced) {
+        log.success(`Synced templates to ${harnesses.join(', ')}`);
     }
-    // Install GitHub issue template for structured agent-ready issues
+    // --- Step 9: GitHub issue template ---
+    log.step('Step 9: Issue template');
     const templateDir = join('.github', 'ISSUE_TEMPLATE');
     const templateFile = join(templateDir, 'agent-ready.yml');
     if (!existsSync(templateFile)) {
         mkdirSync(templateDir, { recursive: true });
         writeFileSync(templateFile, ISSUE_TEMPLATE);
-        log.success('Created GitHub issue template: .github/ISSUE_TEMPLATE/agent-ready.yml');
+        log.success('Created GitHub issue template');
     }
-    // Sync agent assets to all configured harnesses (default to claude-code + codex on first init)
-    const initConfig = loadConfig();
-    const initHarnesses = initConfig.harnesses.length > 0
-        ? initConfig.harnesses
-        : ['claude-code', 'codex'];
-    const syncResult = syncAgentAssets(initHarnesses);
-    if (syncResult.synced) {
-        log.success('Agent assets synced across .claude/ and .agents/');
+    else {
+        log.info('Issue template already exists');
+    }
+    // --- Step 10: Commit ---
+    log.step('Step 10: Commit generated files');
+    const statusResult = exec('git status --porcelain .alpha-loop/ .claude/ .agents/ .codex/ CLAUDE.md AGENTS.md .gitignore .github/');
+    if (statusResult.stdout.trim()) {
+        exec('git add .alpha-loop/ .claude/ .agents/ .codex/ CLAUDE.md AGENTS.md .gitignore .github/ 2>/dev/null || true');
+        const diffCheck = exec('git diff --cached --quiet');
+        if (diffCheck.exitCode !== 0) {
+            exec('git commit -m "chore: initialize alpha-loop (skills, agents, context, instructions)"');
+            log.success('Committed generated files');
+        }
+    }
+    else {
+        log.info('No new files to commit');
     }
+    log.success('Alpha-loop initialization complete!');
 }
 //# sourceMappingURL=init.js.map

package/dist/commands/init.js.map

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package/dist/commands/review.js

@@ -11,6 +11,7 @@ import { formatTimestamp } from '../lib/shell.js';
 import { spawnAgent } from '../lib/agent.js';
 import { createPR } from '../lib/github.js';
 import { syncAgentAssets } from './sync.js';
+import { findDistributionTemplatesDir, diffSkills } from '../lib/templates.js';
 /** Directories that proposed changes are allowed to target. */
 const ALLOWED_PREFIXES = [
     '.alpha-loop/templates/skills/',
@@ -497,6 +498,33 @@ export async function reviewCommand(options) {
     });
     log.success(`${safeProposals.length} improvement(s) proposed`);
     displayProposals(safeProposals);
+    // --- Check for skill upgrades from distribution templates ---
+    const distTemplatesDir = findDistributionTemplatesDir();
+    if (distTemplatesDir) {
+        const distSkillsDir = join(distTemplatesDir, 'skills');
+        const projectSkillsDir = join(projectDir, '.alpha-loop', 'templates', 'skills');
+        const upgrades = diffSkills(distSkillsDir, projectSkillsDir);
+        if (upgrades.length > 0) {
+            log.info('');
+            log.step(`Skill upgrades available (${upgrades.length}):`);
+            for (const u of upgrades) {
+                log.info(`  ${u.status === 'new' ? '[NEW]' : '[UPDATE]'} ${u.name}`);
+            }
+            if (options.apply) {
+                // Apply skill upgrades
+                mkdirSync(projectSkillsDir, { recursive: true });
+                for (const u of upgrades) {
+                    const destDir = join(projectSkillsDir, u.name);
+                    mkdirSync(destDir, { recursive: true });
+                    writeFileSync(join(destDir, 'SKILL.md'), u.distContent);
+                    log.success(`Upgraded skill: ${u.name}`);
+                }
+            }
+            else {
+                log.info('  Run with --apply to install these upgrades.');
+            }
+        }
+    }
     // --- Apply or save ---
     if (options.apply) {
         if (!config.repo) {

package/dist/commands/review.js.map

@@ -1 +1 @@
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package/dist/commands/scan.d.ts

@@ -1 +1,6 @@
 export declare function scanCommand(): void;
+/**
+ * Generate or update the instructions file at .alpha-loop/templates/instructions.md.
+ * If no existing file, generates from scratch. If existing, merges with fresh scan.
+ */
+export declare function generateInstructions(projectDir: string, model: string): void;

package/dist/commands/scan.js

@@ -1,5 +1,6 @@
 import * as fs from 'node:fs';
 import * as path from 'node:path';
+import { tmpdir } from 'node:os';
 import { exec } from '../lib/shell.js';
 import { log } from '../lib/logger.js';
 import { assertSafeShellArg, loadConfig } from '../lib/config.js';
@@ -25,12 +26,66 @@ const SCAN_PROMPT = `Analyze this codebase and produce a concise project context
 - Recent changes: (will be filled in by the loop)
 
 Keep each section to 3-5 bullet points. Be specific to THIS codebase, not generic advice. Under 400 words total.`;
+/**
+ * Prompt for generating the lean instructions file.
+ * Contains ONLY project context — procedural content (testing, git, security) lives in skills.
+ */
+const INSTRUCTIONS_PROMPT = `Analyze this codebase and produce a concise project instructions file for AI coding agents working in this repo.
+
+Output ONLY this markdown structure with the marker comment on the first line:
+
+<!-- managed by alpha-loop -->
+# [Project Name]
+
+## Overview
+[2-3 sentences: what this project is, what it does, who it's for]
+
+## Tech Stack
+- Language: [e.g., TypeScript (strict mode, ESM)]
+- Runtime: [e.g., Node.js 20+]
+- Framework: [e.g., Express 5, React 19]
+- Package manager: [e.g., pnpm]
+- Key dependencies: [top 3-5 important dependencies]
+
+## Directory Structure
+[List key directories and what they contain — only the important ones, not every folder]
+
+## Code Style
+[Naming conventions, import ordering, formatting rules, architectural patterns — be specific to THIS codebase]
+
+## Non-Negotiables
+[Critical rules that must never be violated — security, data safety, patterns that break things if not followed]
+
+IMPORTANT RULES:
+- Do NOT include testing procedures, git workflow, code review checklists, or security scanning procedures — those belong in separate skills, not here.
+- Do NOT include build/deploy commands — those are operational, not instructional.
+- Keep it under 150 lines. Be specific to THIS codebase, not generic advice.
+- The marker comment "<!-- managed by alpha-loop -->" MUST be the very first line.`;
+/**
+ * Prompt for merging an existing instructions file with fresh scan results.
+ */
+const INSTRUCTIONS_MERGE_PROMPT = `You are updating a project instructions file for AI coding agents.
+
+Below is the EXISTING instructions file and the CURRENT state of the codebase. Your job is to:
+1. PRESERVE any user customizations and project-specific rules in the existing file
+2. UPDATE sections that are stale or incorrect based on the current codebase
+3. ADD any important new context discovered in the codebase
+4. REMOVE information that is no longer accurate
+
+The marker comment "<!-- managed by alpha-loop -->" MUST remain as the very first line.
+
+IMPORTANT: Do NOT add testing procedures, git workflow, code review checklists, or security scanning — those belong in skills, not instructions. Keep the same 5-section structure (Overview, Tech Stack, Directory Structure, Code Style, Non-Negotiables). Keep it under 150 lines.
+
+## EXISTING INSTRUCTIONS FILE:
+
+`;
 export function scanCommand() {
     const projectDir = process.cwd();
     const contextDir = path.join(projectDir, '.alpha-loop');
     const contextFile = path.join(contextDir, 'context.md');
     const config = loadConfig();
     fs.mkdirSync(contextDir, { recursive: true });
+    // --- Generate project context ---
     log.step('Scanning codebase for project context...');
     const model = assertSafeShellArg(config.model ?? 'opus', 'model');
     const result = exec(`echo ${JSON.stringify(SCAN_PROMPT)} | claude -p --model ${model} --dangerously-skip-permissions --output-format text 2>/dev/null`, { cwd: projectDir });
@@ -46,5 +101,79 @@ export function scanCommand() {
     else {
         log.error(`Project context generation failed: ${result.stderr || 'empty output'}`);
     }
+    // --- Generate instructions file ---
+    generateInstructions(projectDir, model);
+}
+/**
+ * Generate or update the instructions file at .alpha-loop/templates/instructions.md.
+ * If no existing file, generates from scratch. If existing, merges with fresh scan.
+ */
+export function generateInstructions(projectDir, model) {
+    const templatesDir = path.join(projectDir, '.alpha-loop', 'templates');
+    fs.mkdirSync(templatesDir, { recursive: true });
+    const instructionsFile = path.join(templatesDir, 'instructions.md');
+    const existing = fs.existsSync(instructionsFile)
+        ? fs.readFileSync(instructionsFile, 'utf-8')
+        : null;
+    if (existing) {
+        // Merge mode: preserve user customizations, update stale content
+        log.step('Updating instructions file...');
+        // Back up existing before merge
+        fs.writeFileSync(instructionsFile + '.bak', existing, 'utf-8');
+        const mergePrompt = INSTRUCTIONS_MERGE_PROMPT + existing +
+            '\n\n## OUTPUT:\nProduce the updated instructions file. Output ONLY the markdown content, nothing else.';
+        // Write prompt to temp file to avoid shell injection from file content
+        const safeModel = assertSafeShellArg(model, 'model');
+        const promptFile = path.join(tmpdir(), `alpha-loop-merge-${Date.now()}.txt`);
+        fs.writeFileSync(promptFile, mergePrompt, 'utf-8');
+        const mergeResult = exec(`claude -p --model ${safeModel} --dangerously-skip-permissions --output-format text < "${promptFile}" 2>/dev/null`, { cwd: projectDir });
+        try {
+            fs.unlinkSync(promptFile);
+        }
+        catch { /* cleanup best-effort */ }
+        if (mergeResult.exitCode === 0 && mergeResult.stdout.trim()) {
+            let output = mergeResult.stdout.trim();
+            // Ensure marker is present
+            if (!output.startsWith('<!-- managed by alpha-loop -->')) {
+                output = '<!-- managed by alpha-loop -->\n' + output;
+            }
+            fs.writeFileSync(instructionsFile, output + '\n');
+            log.success('Instructions file updated (backup at instructions.md.bak)');
+        }
+        else {
+            log.warn('Instructions merge failed, keeping existing file');
+        }
+    }
+    else {
+        // Fresh generation
+        log.step('Generating baseline instructions file...');
+        const safeModel = assertSafeShellArg(model, 'model');
+        const genPromptFile = path.join(tmpdir(), `alpha-loop-gen-${Date.now()}.txt`);
+        fs.writeFileSync(genPromptFile, INSTRUCTIONS_PROMPT, 'utf-8');
+        const genResult = exec(`claude -p --model ${safeModel} --dangerously-skip-permissions --output-format text < "${genPromptFile}" 2>/dev/null`, { cwd: projectDir });
+        try {
+            fs.unlinkSync(genPromptFile);
+        }
+        catch { /* cleanup best-effort */ }
+        if (genResult.exitCode === 0 && genResult.stdout.trim()) {
+            let output = genResult.stdout.trim();
+            if (!output.startsWith('<!-- managed by alpha-loop -->')) {
+                output = '<!-- managed by alpha-loop -->\n' + output;
+            }
+            fs.writeFileSync(instructionsFile, output + '\n');
+            log.success(`Instructions file generated: ${instructionsFile}`);
+        }
+        else if (genResult.stdout?.trim()) {
+            let output = genResult.stdout.trim();
+            if (!output.startsWith('<!-- managed by alpha-loop -->')) {
+                output = '<!-- managed by alpha-loop -->\n' + output;
+            }
+            fs.writeFileSync(instructionsFile, output + '\n');
+            log.warn('Claude exited with errors but produced instructions output');
+        }
+        else {
+            log.warn('Instructions generation failed — will retry on next scan');
+        }
+    }
 }
 //# sourceMappingURL=scan.js.map

package/dist/commands/scan.js.map

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package/dist/commands/sync.d.ts

@@ -1,8 +1,11 @@
 export type HarnessConfig = {
     skillsDir: string;
     agentsDir?: string;
+    instructionsFile?: string;
 };
 export declare const HARNESS_REGISTRY: Record<string, HarnessConfig>;
+/** Marker that identifies files managed by alpha-loop (safe to overwrite). */
+export declare const MANAGED_MARKER = "<!-- managed by alpha-loop -->";
 export type SyncResult = {
     synced: boolean;
     docSynced: boolean;
@@ -23,7 +26,6 @@ export declare function syncAgentAssets(harnesses: string[], options?: {
  *
  * Moves:
  *   skills/          → .alpha-loop/templates/skills/
- *   AGENTS.md        → .alpha-loop/templates/instructions.md
  *   .claude/agents/  → .alpha-loop/templates/agents/
  *
  * Does NOT delete the originals — the next sync run will recreate them

package/dist/commands/sync.js

@@ -1,13 +1,13 @@
 /**
- * Sync Command — keep skills and sub-agents in sync across coding harnesses.
+ * Sync Command — keep skills, sub-agents, and instructions in sync across coding harnesses.
  *
  * Source of truth: .alpha-loop/templates/
  *   skills/          → each harness's skillsDir
  *   agents/          → each harness's agentsDir (if defined)
+ *   instructions.md  → each harness's instructionsFile (e.g., CLAUDE.md, AGENTS.md)
  *
- * CLAUDE.md and AGENTS.md are project-owned files and are NOT synced.
- * Alpha-loop's operational instructions live in the sub-agent prompts
- * (.claude/agents/implementer.md, etc.), not in the project instructions file.
+ * Instructions files are only overwritten if they contain the "<!-- managed by alpha-loop -->"
+ * marker. Existing hand-written CLAUDE.md/AGENTS.md files are never touched.
  *
  * Harnesses to sync are read from the `harnesses` array supplied by the caller
  * (typically loaded from .alpha-loop.yaml). Only harnesses that exist in the
@@ -17,46 +17,46 @@ import { existsSync, copyFileSync, mkdirSync, readdirSync, statSync, readFileSyn
 import { join } from 'node:path';
 import { log } from '../lib/logger.js';
 export const HARNESS_REGISTRY = {
-    amp: { skillsDir: '.agents/skills' },
-    antigravity: { skillsDir: '.agents/skills' },
+    amp: { skillsDir: '.agents/skills', instructionsFile: 'AGENTS.md' },
+    antigravity: { skillsDir: '.agents/skills', instructionsFile: 'AGENTS.md' },
     augment: { skillsDir: '.augment/skills' },
     bob: { skillsDir: '.bob/skills' },
-    'claude-code': { skillsDir: '.claude/skills', agentsDir: '.claude/agents' },
+    'claude-code': { skillsDir: '.claude/skills', agentsDir: '.claude/agents', instructionsFile: 'CLAUDE.md' },
     openclaw: { skillsDir: 'skills' },
-    cline: { skillsDir: '.agents/skills' },
-    warp: { skillsDir: '.agents/skills' },
+    cline: { skillsDir: '.agents/skills', instructionsFile: 'AGENTS.md' },
+    warp: { skillsDir: '.agents/skills', instructionsFile: 'AGENTS.md' },
     codebuddy: { skillsDir: '.codebuddy/skills' },
-    codex: { skillsDir: '.agents/skills', agentsDir: '.codex/agents' },
+    codex: { skillsDir: '.agents/skills', agentsDir: '.codex/agents', instructionsFile: 'AGENTS.md' },
     'command-code': { skillsDir: '.commandcode/skills' },
     continue: { skillsDir: '.continue/skills' },
     cortex: { skillsDir: '.cortex/skills' },
     crush: { skillsDir: '.crush/skills' },
-    cursor: { skillsDir: '.agents/skills' },
-    deepagents: { skillsDir: '.agents/skills' },
+    cursor: { skillsDir: '.agents/skills', instructionsFile: 'AGENTS.md' },
+    deepagents: { skillsDir: '.agents/skills', instructionsFile: 'AGENTS.md' },
     droid: { skillsDir: '.factory/skills' },
-    firebender: { skillsDir: '.agents/skills' },
-    'gemini-cli': { skillsDir: '.agents/skills' },
-    'github-copilot': { skillsDir: '.agents/skills' },
+    firebender: { skillsDir: '.agents/skills', instructionsFile: 'AGENTS.md' },
+    'gemini-cli': { skillsDir: '.agents/skills', instructionsFile: 'AGENTS.md' },
+    'github-copilot': { skillsDir: '.agents/skills', instructionsFile: 'AGENTS.md' },
     goose: { skillsDir: '.goose/skills' },
     junie: { skillsDir: '.junie/skills' },
     'iflow-cli': { skillsDir: '.iflow/skills' },
     kilo: { skillsDir: '.kilocode/skills' },
-    'kimi-cli': { skillsDir: '.agents/skills' },
+    'kimi-cli': { skillsDir: '.agents/skills', instructionsFile: 'AGENTS.md' },
     'kiro-cli': { skillsDir: '.kiro/skills' },
     kode: { skillsDir: '.kode/skills' },
     mcpjam: { skillsDir: '.mcpjam/skills' },
     'mistral-vibe': { skillsDir: '.vibe/skills' },
     mux: { skillsDir: '.mux/skills' },
-    opencode: { skillsDir: '.agents/skills' },
+    opencode: { skillsDir: '.agents/skills', instructionsFile: 'AGENTS.md' },
     openhands: { skillsDir: '.openhands/skills' },
     pi: { skillsDir: '.pi/skills' },
     qoder: { skillsDir: '.qoder/skills' },
     'qwen-code': { skillsDir: '.qwen/skills' },
-    replit: { skillsDir: '.agents/skills' },
+    replit: { skillsDir: '.agents/skills', instructionsFile: 'AGENTS.md' },
     roo: { skillsDir: '.roo/skills' },
     trae: { skillsDir: '.trae/skills' },
     'trae-cn': { skillsDir: '.trae/skills' },
-    universal: { skillsDir: '.agents/skills' },
+    universal: { skillsDir: '.agents/skills', instructionsFile: 'AGENTS.md' },
     windsurf: { skillsDir: '.windsurf/skills' },
     zencoder: { skillsDir: '.zencoder/skills' },
     neovate: { skillsDir: '.neovate/skills' },
@@ -69,6 +69,9 @@ export const HARNESS_REGISTRY = {
 const TEMPLATES_DIR = '.alpha-loop/templates';
 const TEMPLATE_SKILLS_SUBDIR = 'skills';
 const TEMPLATE_AGENTS_SUBDIR = 'agents';
+const TEMPLATE_INSTRUCTIONS_FILE = 'instructions.md';
+/** Marker that identifies files managed by alpha-loop (safe to overwrite). */
+export const MANAGED_MARKER = '<!-- managed by alpha-loop -->';
 // Legacy root-level fallbacks
 const LEGACY_SKILLS_DIR = 'skills';
 const LEGACY_CLAUDE_AGENTS_DIR = '.claude/agents';
@@ -142,10 +145,12 @@ function resolveTemplateSources(projectDir) {
     const templatesBase = join(projectDir, TEMPLATES_DIR);
     const templateSkills = join(templatesBase, TEMPLATE_SKILLS_SUBDIR);
     const templateAgents = join(templatesBase, TEMPLATE_AGENTS_SUBDIR);
+    const templateInstructions = join(templatesBase, TEMPLATE_INSTRUCTIONS_FILE);
     if (existsSync(templatesBase)) {
         return {
             skillsDir: templateSkills,
             agentsDir: templateAgents,
+            instructionsFile: templateInstructions,
             isLegacy: false,
         };
     }
@@ -153,10 +158,11 @@ function resolveTemplateSources(projectDir) {
     const legacySkills = join(projectDir, LEGACY_SKILLS_DIR);
     if (existsSync(legacySkills)) {
         log.warn(`Legacy layout detected (${LEGACY_SKILLS_DIR}/ at project root). ` +
-            `Run "alpha-loop migrate" to move them to ${TEMPLATES_DIR}/.`);
+            `Run "alpha-loop init" to migrate to ${TEMPLATES_DIR}/.`);
         return {
             skillsDir: legacySkills,
             agentsDir: join(projectDir, LEGACY_CLAUDE_AGENTS_DIR),
+            instructionsFile: '', // No instructions in legacy layout
             isLegacy: true,
         };
     }
@@ -213,6 +219,32 @@ export function syncAgentAssets(harnesses, options = {}) {
                 result.synced = true;
             }
         }
+        // -- Instructions file --
+        if (config.instructionsFile && sources.instructionsFile && existsSync(sources.instructionsFile)) {
+            const targetFile = join(projectDir, config.instructionsFile);
+            if (!filesMatch(sources.instructionsFile, targetFile)) {
+                // Safety: only overwrite if the target doesn't exist or contains the managed marker
+                const targetExists = existsSync(targetFile);
+                const targetManaged = targetExists &&
+                    readFileSync(targetFile, 'utf-8').startsWith(MANAGED_MARKER);
+                if (!targetExists || targetManaged) {
+                    if (check) {
+                        log.warn(`Drift [${harness}]: ${config.instructionsFile} differs from template instructions.md`);
+                    }
+                    else {
+                        mkdirSync(join(targetFile, '..'), { recursive: true });
+                        copyFileSync(sources.instructionsFile, targetFile);
+                        log.info(`Synced [${harness}] instructions.md → ${config.instructionsFile}`);
+                    }
+                    result.docSynced = true;
+                    result.synced = true;
+                }
+                else {
+                    log.warn(`Skipping ${config.instructionsFile} — file exists without alpha-loop marker. ` +
+                        `Run "alpha-loop scan" to generate a managed instructions file.`);
+                }
+            }
+        }
     }
     return result;
 }
@@ -221,7 +253,6 @@ export function syncAgentAssets(harnesses, options = {}) {
  *
  * Moves:
  *   skills/          → .alpha-loop/templates/skills/
- *   AGENTS.md        → .alpha-loop/templates/instructions.md
  *   .claude/agents/  → .alpha-loop/templates/agents/
  *
  * Does NOT delete the originals — the next sync run will recreate them

package/dist/commands/sync.js.map

@@ -1 +1 @@
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package/dist/lib/templates.d.ts

@@ -0,0 +1,16 @@
+/**
+ * Find the distribution templates directory shipped with the alpha-loop npm package.
+ * Walks up from the CLI entrypoint, following symlinks for global installs.
+ */
+export declare function findDistributionTemplatesDir(): string | null;
+export type SkillDiff = {
+    name: string;
+    status: 'new' | 'updated';
+    distContent: string;
+    projectContent?: string;
+};
+/**
+ * Compare project skills against distribution templates.
+ * Returns skills that are new or have changed content.
+ */
+export declare function diffSkills(distSkillsDir: string, projectSkillsDir: string): SkillDiff[];

package/dist/lib/templates.js

@@ -0,0 +1,59 @@
+/**
+ * Templates — shared utilities for locating distribution templates
+ * and comparing project skills against them.
+ */
+import { existsSync, readdirSync, readFileSync, realpathSync } from 'node:fs';
+import { join, dirname } from 'node:path';
+/**
+ * Find the distribution templates directory shipped with the alpha-loop npm package.
+ * Walks up from the CLI entrypoint, following symlinks for global installs.
+ */
+export function findDistributionTemplatesDir() {
+    let startDir;
+    try {
+        startDir = dirname(realpathSync(process.argv[1]));
+    }
+    catch {
+        startDir = process.cwd();
+    }
+    let dir = startDir;
+    for (let i = 0; i < 5; i++) {
+        const candidate = join(dir, 'templates');
+        if (existsSync(candidate))
+            return candidate;
+        const parent = dirname(dir);
+        if (parent === dir)
+            break;
+        dir = parent;
+    }
+    return null;
+}
+/**
+ * Compare project skills against distribution templates.
+ * Returns skills that are new or have changed content.
+ */
+export function diffSkills(distSkillsDir, projectSkillsDir) {
+    if (!existsSync(distSkillsDir))
+        return [];
+    const diffs = [];
+    const distSkills = readdirSync(distSkillsDir, { withFileTypes: true })
+        .filter((d) => d.isDirectory());
+    for (const entry of distSkills) {
+        const distSkillFile = join(distSkillsDir, entry.name, 'SKILL.md');
+        if (!existsSync(distSkillFile))
+            continue;
+        const distContent = readFileSync(distSkillFile, 'utf-8');
+        const projectSkillFile = join(projectSkillsDir, entry.name, 'SKILL.md');
+        if (!existsSync(projectSkillFile)) {
+            diffs.push({ name: entry.name, status: 'new', distContent });
+        }
+        else {
+            const projectContent = readFileSync(projectSkillFile, 'utf-8');
+            if (projectContent !== distContent) {
+                diffs.push({ name: entry.name, status: 'updated', distContent, projectContent });
+            }
+        }
+    }
+    return diffs;
+}
+//# sourceMappingURL=templates.js.map

package/dist/lib/templates.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@bradtaylorsf/alpha-loop",
-  "version": "1.0.1",
+  "version": "1.1.0",
   "description": "Agent-agnostic automated development loop: Plan → Build → Test → Review → Ship",
   "type": "module",
   "packageManager": "pnpm@9.0.0",