@autonomos/cli 0.0.1 → 0.0.3

package/dist/index.mjs

@@ -1,5 +1,5 @@
 #!/usr/bin/env node
-import{Command as e}from"commander";import t from"picocolors";import{AGENT_FILE as n,AUTONOMOS_DIR as r,MANIFEST_FILE as i,PROTOCOL_FILE as a,PROTOCOL_TEMPLATE as o,PROTOCOL_VERSION as s,TASKS_FILE as c,TASKS_TEMPLATE as l,TaskParser as u,WORKLOGS_DIR as d,createManifest as f,generateAgentTemplate as p,generateManifestContent as m,parseManifest as h}from"@autonomos/core";import{existsSync as g,mkdirSync as _,readFileSync as v,readdirSync as y,statSync as b,writeFileSync as x}from"node:fs";import{basename as S,join as C,relative as w}from"node:path";function T(e){let t=e;for(;t!==`/`;){if(g(C(t,r))||g(C(t,`.git`)))return t;t=C(t,`..`)}return null}function E(e,t,r=0){let i=[],a=C(e,n);g(a)&&i.push({path:a,relativePath:w(t,a)||n,depth:r});try{let n=y(e);for(let a of n){if(a.startsWith(`.`)||a===`node_modules`||a===`dist`||a===`build`)continue;let n=C(e,a);try{b(n).isDirectory()&&i.push(...E(n,t,r+1))}catch{}}}catch{}return i}function D(e,t){if(e.length===0)return`  (no AGENT.md files found)`;let n=[],r=S(t);n.push(`📁 ${r}/`);for(let t=0;t<e.length;t++){let r=e[t],i=t===e.length-1?`└── `:`├── `,a=`    `.repeat(r.depth);n.push(`${a}${i}📄 ${r.relativePath}`)}return n.join(`
+import{Command as e}from"commander";import t from"picocolors";import{AGENT_FILE as n,AUTONOMOS_DIR as r,MANIFEST_FILE as i,PROTOCOL_FILE as a,PROTOCOL_TEMPLATE as o,PROTOCOL_VERSION as s,TASKS_FILE as c,TASKS_TEMPLATE as l,TaskParser as u,WORKLOGS_DIR as d,createManifest as f,generateAgentTemplate as p,generateManifestContent as m,parseManifest as h}from"@autonomos/core";import{existsSync as g,mkdirSync as _,readFileSync as v,readdirSync as y,statSync as b,writeFileSync as x}from"node:fs";import{basename as S,join as C,relative as w}from"node:path";function T(e){let t=e;for(;t!==`/`;){if(g(C(t,r))||g(C(t,`.git`)))return t;t=C(t,`..`)}return null}function E(e,t,r=0){let i=[],a=C(e,n);g(a)&&i.push({path:a,relativePath:w(t,a)||n,depth:r});try{let n=y(e);for(let a of n){if(a.startsWith(`.`)||a===`node_modules`||a===`dist`||a===`build`)continue;let n=C(e,a);try{b(n).isDirectory()&&i.push(...E(n,t,r+1))}catch{}}}catch{}return i}function D(e,t){if(e.length===0)return`  (no AGENT.md files found)`;let r=S(t),i={name:r,isAgent:!1,children:{}};for(let t of e){let e=t.relativePath.split(`/`),r=i;for(let t=0;t<e.length;t++){let i=e[t],a=i===n;r.children[i]||(r.children[i]={name:i,isAgent:a,children:{}}),r=r.children[i]}}let a=[];a.push(`📁 ${r}/`);function o(e,t=``,n=!0){let r=Object.values(e.children);r.sort((e,t)=>!e.isAgent&&t.isAgent?-1:e.isAgent&&!t.isAgent?1:e.name.localeCompare(t.name)),r.forEach((e,n)=>{let i=n===r.length-1,s=i?`└── `:`├── `,c=e.isAgent?`📄`:`📁`,l=e.isAgent?e.name:`${e.name}/`;a.push(`${t}${s}${c} ${l}`),e.isAgent||o(e,t+(i?`    `:`│   `),i)})}return o(i),a.join(`
 `)}function O(e={}){let t=e.cwd??process.cwd(),n;if(e.all){let e=T(t);if(!e)return{success:!1,message:`Could not find project root (.autonomos or .git directory).`};n=e}else n=t;let r=E(n,n);if(r.length===0)return{success:!0,message:`No AGENT.md files found.`,count:0};let i=D(r,n);return{success:!0,message:`Found ${r.length} AGENT.md file(s)`,tree:i,count:r.length}}function k(e={}){let t=e.cwd??process.cwd(),u=e.dryRun??!1,h=[],v=[];g(C(t,`.git`))||v.push("No Git repository detected. Consider running `git init` first.");let y=C(t,r);if(g(y))return{success:!1,message:`Project already initialized with Protocol v${s}. Use \`autonomos update\` to update.`,created:[],warnings:[],dryRun:u};if(u)return h.push(r),h.push(`${r}/${d}`),h.push(`${r}/${i}`),h.push(`${r}/${a}`),h.push(`${r}/${c}`),g(C(t,n))?v.push(`${n} already exists, would skip.`):h.push(n),{success:!0,message:`Would initialize project with Agent Protocol v${s}`,created:h,warnings:v,dryRun:!0};_(y,{recursive:!0}),h.push(r),_(C(y,d),{recursive:!0}),h.push(`${r}/${d}`);let b=f(`0.0.1`);x(C(y,i),m(b)),h.push(`${r}/${i}`),x(C(y,a),o),h.push(`${r}/${a}`),x(C(y,c),l),h.push(`${r}/${c}`);let S=C(t,n);return g(S)?v.push(`${n} already exists, skipping.`):(x(S,p(t.split(`/`).pop()??`Project`)),h.push(n)),{success:!0,message:`Project initialized with Agent Protocol v${s}`,created:h,warnings:v,dryRun:!1}}function A(e={}){let t=C(e.cwd??process.cwd(),r),n=C(t,i);if(!g(n))return{success:!1,message:"Project not initialized. Run `autonomos init` first.",initialized:!1};let a;try{a=h(v(n,`utf-8`))}catch{return{success:!1,message:`Could not read manifest.json`,initialized:!0}}let o,s=C(t,c);if(g(s))try{let e=v(s,`utf-8`),t=u.parse(e);o={total:t.length,todo:t.filter(e=>e.status===`TODO`).length,inProgress:t.filter(e=>e.status===`IN_PROGRESS`).length,done:t.filter(e=>e.status===`DONE`).length,blocked:t.filter(e=>e.status===`BLOCKED`).length}}catch{}return{success:!0,message:`Project status retrieved`,protocolVersion:a.protocolVersion,cliVersion:a.cliVersion,initialized:!0,taskSummary:o}}function j(e,t){let n=e.split(`.`).map(Number),r=t.split(`.`).map(Number);for(let e=0;e<3;e++){let t=n[e]??0,i=r[e]??0;if(t<i)return-1;if(t>i)return 1}return 0}function M(e={}){let t=C(e.cwd??process.cwd(),r),n=C(t,i);if(!g(n))return{success:!1,message:"Project not initialized. Run `autonomos init` first."};let c=h(v(n,`utf-8`)),l=c.protocolVersion,u=j(l,s);return u===0?{success:!0,message:`Already up to date (Protocol v${s})`,previousVersion:l,newVersion:s}:u>0?{success:!1,message:`This project uses Protocol v${l}, but your CLI only knows v${s}. Update your CLI with \`npm i -g @autonomos/cli\`.`,previousVersion:l,newVersion:s,cliOutdated:!0}:(x(C(t,a),o),x(n,m({...c,protocolVersion:s,cliVersion:`0.0.1`,lastUpdated:new Date().toISOString()})),{success:!0,message:`Protocol updated: v${l} → v${s}`,previousVersion:l,newVersion:s})}const N=`0.0.1`,P=new e;P.name(`autonomos`).description(t.cyan(`CLI for the Autonomos Agent Protocol
 
 The Agent Protocol is a specification for AI agents to interact with codebases

package/package.json

@@ -1,15 +1,43 @@
 {
   "name": "@autonomos/cli",
-  "version": "0.0.1",
+  "version": "0.0.3",
   "description": "CLI tool for the Autonomos Agent Protocol",
   "type": "module",
   "bin": {
     "autonomos": "./dist/index.mjs"
   },
+  "keywords": [
+    "cli",
+    "agent",
+    "protocol",
+    "ai",
+    "workflow",
+    "ai-agent",
+    "autonomos"
+  ],
+  "author": "Autonomos",
+  "license": "MIT",
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/saoudi-h/autonomos.git",
+    "directory": "packages/cli"
+  },
+  "bugs": {
+    "url": "https://github.com/saoudi-h/autonomos/issues"
+  },
+  "homepage": "https://github.com/saoudi-h/autonomos/tree/main/packages/cli#readme",
+  "publishConfig": {
+    "access": "public"
+  },
+  "files": [
+    "dist",
+    "README.md",
+    "LICENSE"
+  ],
   "dependencies": {
     "commander": "^14.0.2",
     "picocolors": "1.1.1",
-    "@autonomos/core": "0.0.1"
+    "@autonomos/core": "0.0.2"
   },
   "devDependencies": {
     "@types/node": "^25.0.3",
@@ -27,12 +55,12 @@
   },
   "scripts": {
     "start": "node dist/index.mjs",
-    "build": "tsdown",
+    "build": "tsdown && cp ../../LICENSE .",
     "lint": "eslint . --max-warnings 0",
     "lint:fix": "eslint . --max-warnings 0 --fix",
     "format:check": "prettier \"**/*\" --ignore-unknown --list-different",
     "format:fix": "prettier \"**/*\" --ignore-unknown --write",
-    "clean": "rimraf node_modules dist",
+    "clean": "rimraf node_modules dist LICENSE",
     "typecheck": "tsc -p tsconfig.json --noEmit",
     "test": "vitest",
     "test:ui": "vitest --ui",

package/.turbo/turbo-build.log

@@ -1,16 +0,0 @@
-
-> @autonomos/cli@0.0.1 build /home/runner/work/autonomos/autonomos/packages/cli
-> tsdown
-
-ℹ tsdown v0.18.4 powered by rolldown v1.0.0-beta.57
-ℹ config file: /home/runner/work/autonomos/autonomos/packages/cli/tsdown.config.ts 
-ℹ entry: src/index.ts
-ℹ tsconfig: tsconfig.json
-ℹ Build start
-ℹ Granting execute permission to dist/index.mjs
-ℹ dist/index.mjs    9.19 kB │ gzip: 3.35 kB
-ℹ dist/index.d.mts  0.01 kB │ gzip: 0.03 kB
-ℹ 2 files, total: 9.20 kB
-✔ Build complete in 1088ms
-✔ [publint] No issues found (342ms)
-🙏 Build succeeded!

package/AGENT.md

@@ -1,11 +0,0 @@
-# AGENT CONTEXT: @autonomos/cli
-
-## 🧠 Context & Objectives
-
-This package is the public-facing tool for the Agent Protocol.
-It consumes `@autonomos/core` to perform actions like bootstrapping projects (`init`), updating docs, or parsing tasks.
-
-## ⚙️ Workflow
-
-- **Dependencies:** Uses `commander` for CLI args.
-- **Linkage:** Depends on `workspace:@autonomos/core`.

package/eslint.config.ts

@@ -1,18 +0,0 @@
-import type { Config } from '@repo/eslint'
-import { base } from '@repo/eslint'
-import { defineConfig } from 'eslint/config'
-
-const config: Config[] = defineConfig([
-    ...base,
-    {
-        ignores: [
-            'eslint.config.ts',
-            'eslint-types.d.ts',
-            'prettier.config.mjs',
-            'lint-staged.config.mjs',
-            'lowercase-script.ts',
-        ],
-    },
-])
-
-export default config

package/lint-staged.config.mjs

@@ -1,4 +0,0 @@
-export default {
-    '**/*.{ts,tsx}': ['prettier --write', 'eslint --fix --no-warn-ignored'],
-    '**/*.{json,md,mdx}': 'prettier --write',
-}

package/prettier.config.mjs

@@ -1,3 +0,0 @@
-import baseConfig from '@repo/prettier'
-
-export default baseConfig

package/src/commands/agents.ts

@@ -1,154 +0,0 @@
-import { existsSync, readdirSync, statSync } from 'node:fs'
-import { basename, join, relative } from 'node:path'
-
-import { AGENT_FILE, AUTONOMOS_DIR } from '@autonomos/core'
-
-interface AgentsOptions {
-    cwd?: string
-    all?: boolean
-}
-
-interface AgentEntry {
-    path: string
-    relativePath: string
-    depth: number
-}
-
-/**
- * Find the project root by looking for .autonomos or .git directory
- */
-function findProjectRoot(startDir: string): string | null {
-    let currentDir = startDir
-
-    while (currentDir !== '/') {
-        if (existsSync(join(currentDir, AUTONOMOS_DIR)) || existsSync(join(currentDir, '.git'))) {
-            return currentDir
-        }
-        currentDir = join(currentDir, '..')
-    }
-
-    return null
-}
-
-/**
- * Recursively find all AGENT.md files in a directory
- */
-function findAgentFiles(dir: string, baseDir: string, depth = 0): AgentEntry[] {
-    const entries: AgentEntry[] = []
-
-    // Check if AGENT.md exists in current directory
-    const agentPath = join(dir, AGENT_FILE)
-    if (existsSync(agentPath)) {
-        entries.push({
-            path: agentPath,
-            relativePath: relative(baseDir, agentPath) || AGENT_FILE,
-            depth,
-        })
-    }
-
-    // Scan subdirectories
-    try {
-        const items = readdirSync(dir)
-        for (const item of items) {
-            // Skip hidden directories and node_modules
-            if (
-                item.startsWith('.') ||
-                item === 'node_modules' ||
-                item === 'dist' ||
-                item === 'build'
-            ) {
-                continue
-            }
-
-            const itemPath = join(dir, item)
-            try {
-                if (statSync(itemPath).isDirectory()) {
-                    entries.push(...findAgentFiles(itemPath, baseDir, depth + 1))
-                }
-            } catch {
-                // Skip inaccessible directories
-            }
-        }
-    } catch {
-        // Skip inaccessible directories
-    }
-
-    return entries
-}
-
-/**
- * Format agent entries as a tree structure
- */
-function formatAsTree(entries: AgentEntry[], baseDir: string): string {
-    if (entries.length === 0) {
-        return '  (no AGENT.md files found)'
-    }
-
-    const lines: string[] = []
-    const baseName = basename(baseDir)
-
-    lines.push(`📁 ${baseName}/`)
-
-    // Group entries by their parent directory
-    for (let i = 0; i < entries.length; i++) {
-        const entry = entries[i]
-        const isLast = i === entries.length - 1
-        const prefix = isLast ? '└── ' : '├── '
-        const indent = '    '.repeat(entry.depth)
-
-        lines.push(`${indent}${prefix}📄 ${entry.relativePath}`)
-    }
-
-    return lines.join('\n')
-}
-
-interface AgentsResult {
-    success: boolean
-    message: string
-    tree?: string
-    count?: number
-}
-
-/**
- * List all AGENT.md files in the project
- */
-export function agents(options: AgentsOptions = {}): AgentsResult {
-    const cwd = options.cwd ?? process.cwd()
-
-    // Determine search base
-    let searchBase: string
-
-    if (options.all) {
-        // Find project root
-        const projectRoot = findProjectRoot(cwd)
-        if (!projectRoot) {
-            return {
-                success: false,
-                message: 'Could not find project root (.autonomos or .git directory).',
-            }
-        }
-        searchBase = projectRoot
-    } else {
-        searchBase = cwd
-    }
-
-    // Find all AGENT.md files
-    const entries = findAgentFiles(searchBase, searchBase)
-
-    if (entries.length === 0) {
-        return {
-            success: true,
-            message: 'No AGENT.md files found.',
-            count: 0,
-        }
-    }
-
-    const tree = formatAsTree(entries, searchBase)
-
-    return {
-        success: true,
-        message: `Found ${entries.length} AGENT.md file(s)`,
-        tree,
-        count: entries.length,
-    }
-}

package/src/commands/init.ts

@@ -1,128 +0,0 @@
-import { existsSync, mkdirSync, writeFileSync } from 'node:fs'
-import { join } from 'node:path'
-
-import {
-    AGENT_FILE,
-    AUTONOMOS_DIR,
-    createManifest,
-    generateAgentTemplate,
-    generateManifestContent,
-    MANIFEST_FILE,
-    PROTOCOL_FILE,
-    PROTOCOL_TEMPLATE,
-    PROTOCOL_VERSION,
-    TASKS_FILE,
-    TASKS_TEMPLATE,
-    WORKLOGS_DIR,
-} from '@autonomos/core'
-
-// Get CLI version from package.json
-const CLI_VERSION = '0.0.1' // TODO: Import from package.json
-
-interface InitOptions {
-    cwd?: string
-    dryRun?: boolean
-}
-
-interface InitResult {
-    success: boolean
-    message: string
-    created: string[]
-    warnings: string[]
-    dryRun?: boolean
-}
-
-/**
- * Initialize the Autonomos Agent Protocol in a directory
- */
-export function init(options: InitOptions = {}): InitResult {
-    const cwd = options.cwd ?? process.cwd()
-    const dryRun = options.dryRun ?? false
-    const created: string[] = []
-    const warnings: string[] = []
-
-    // Check for .git
-    const gitDir = join(cwd, '.git')
-    if (!existsSync(gitDir)) {
-        warnings.push('No Git repository detected. Consider running `git init` first.')
-    }
-
-    // Check if already initialized
-    const autonomosDir = join(cwd, AUTONOMOS_DIR)
-    if (existsSync(autonomosDir)) {
-        return {
-            success: false,
-            message: `Project already initialized with Protocol v${PROTOCOL_VERSION}. Use \`autonomos update\` to update.`,
-            created: [],
-            warnings: [],
-            dryRun,
-        }
-    }
-
-    // In dry-run mode, just collect what would be created
-    if (dryRun) {
-        created.push(AUTONOMOS_DIR)
-        created.push(`${AUTONOMOS_DIR}/${WORKLOGS_DIR}`)
-        created.push(`${AUTONOMOS_DIR}/${MANIFEST_FILE}`)
-        created.push(`${AUTONOMOS_DIR}/${PROTOCOL_FILE}`)
-        created.push(`${AUTONOMOS_DIR}/${TASKS_FILE}`)
-
-        const agentPath = join(cwd, AGENT_FILE)
-        if (!existsSync(agentPath)) {
-            created.push(AGENT_FILE)
-        } else {
-            warnings.push(`${AGENT_FILE} already exists, would skip.`)
-        }
-
-        return {
-            success: true,
-            message: `Would initialize project with Agent Protocol v${PROTOCOL_VERSION}`,
-            created,
-            warnings,
-            dryRun: true,
-        }
-    }
-
-    // Create .autonomos directory
-    mkdirSync(autonomosDir, { recursive: true })
-    created.push(AUTONOMOS_DIR)
-
-    // Create worklogs directory
-    const worklogsDir = join(autonomosDir, WORKLOGS_DIR)
-    mkdirSync(worklogsDir, { recursive: true })
-    created.push(`${AUTONOMOS_DIR}/${WORKLOGS_DIR}`)
-
-    // Create manifest.json
-    const manifest = createManifest(CLI_VERSION)
-    const manifestPath = join(autonomosDir, MANIFEST_FILE)
-    writeFileSync(manifestPath, generateManifestContent(manifest))
-    created.push(`${AUTONOMOS_DIR}/${MANIFEST_FILE}`)
-
-    // Create PROTOCOL.md
-    const protocolPath = join(autonomosDir, PROTOCOL_FILE)
-    writeFileSync(protocolPath, PROTOCOL_TEMPLATE)
-    created.push(`${AUTONOMOS_DIR}/${PROTOCOL_FILE}`)
-
-    // Create TASKS.md
-    const tasksPath = join(autonomosDir, TASKS_FILE)
-    writeFileSync(tasksPath, TASKS_TEMPLATE)
-    created.push(`${AUTONOMOS_DIR}/${TASKS_FILE}`)
-
-    // Create AGENT.md at root (only if it doesn't exist)
-    const agentPath = join(cwd, AGENT_FILE)
-    if (!existsSync(agentPath)) {
-        const projectName = cwd.split('/').pop() ?? 'Project'
-        writeFileSync(agentPath, generateAgentTemplate(projectName))
-        created.push(AGENT_FILE)
-    } else {
-        warnings.push(`${AGENT_FILE} already exists, skipping.`)
-    }
-
-    return {
-        success: true,
-        message: `Project initialized with Agent Protocol v${PROTOCOL_VERSION}`,
-        created,
-        warnings,
-        dryRun: false,
-    }
-}

package/src/commands/status.ts

@@ -1,94 +0,0 @@
-import { existsSync, readFileSync } from 'node:fs'
-import { join } from 'node:path'
-
-import {
-    AUTONOMOS_DIR,
-    MANIFEST_FILE,
-    parseManifest,
-    TaskParser,
-    TASKS_FILE,
-    type Manifest,
-} from '@autonomos/core'
-
-interface StatusOptions {
-    cwd?: string
-}
-
-interface TaskSummary {
-    total: number
-    todo: number
-    inProgress: number
-    done: number
-    blocked: number
-}
-
-interface StatusResult {
-    success: boolean
-    message: string
-    protocolVersion?: string
-    cliVersion?: string
-    initialized: boolean
-    taskSummary?: TaskSummary
-}
-
-/**
- * Get project status and task summary
- */
-export function status(options: StatusOptions = {}): StatusResult {
-    const cwd = options.cwd ?? process.cwd()
-
-    // Check if initialized
-    const autonomosDir = join(cwd, AUTONOMOS_DIR)
-    const manifestPath = join(autonomosDir, MANIFEST_FILE)
-
-    if (!existsSync(manifestPath)) {
-        return {
-            success: false,
-            message: 'Project not initialized. Run `autonomos init` first.',
-            initialized: false,
-        }
-    }
-
-    // Read manifest
-    let manifest: Manifest
-    try {
-        const manifestContent = readFileSync(manifestPath, 'utf-8')
-        manifest = parseManifest(manifestContent)
-    } catch {
-        return {
-            success: false,
-            message: 'Could not read manifest.json',
-            initialized: true,
-        }
-    }
-
-    // Parse tasks
-    let taskSummary: TaskSummary | undefined
-    const tasksPath = join(autonomosDir, TASKS_FILE)
-
-    if (existsSync(tasksPath)) {
-        try {
-            const tasksContent = readFileSync(tasksPath, 'utf-8')
-            const tasks = TaskParser.parse(tasksContent)
-
-            taskSummary = {
-                total: tasks.length,
-                todo: tasks.filter(t => t.status === 'TODO').length,
-                inProgress: tasks.filter(t => t.status === 'IN_PROGRESS').length,
-                done: tasks.filter(t => t.status === 'DONE').length,
-                blocked: tasks.filter(t => t.status === 'BLOCKED').length,
-            }
-        } catch {
-            // Tasks file exists but couldn't be parsed
-        }
-    }
-
-    return {
-        success: true,
-        message: 'Project status retrieved',
-        protocolVersion: manifest.protocolVersion,
-        cliVersion: manifest.cliVersion,
-        initialized: true,
-        taskSummary,
-    }
-}

package/src/commands/update.ts

@@ -1,111 +0,0 @@
-import { existsSync, readFileSync, writeFileSync } from 'node:fs'
-import { join } from 'node:path'
-
-import {
-    AUTONOMOS_DIR,
-    generateManifestContent,
-    MANIFEST_FILE,
-    parseManifest,
-    PROTOCOL_FILE,
-    PROTOCOL_TEMPLATE,
-    PROTOCOL_VERSION,
-    type Manifest,
-} from '@autonomos/core'
-
-// Get CLI version from package.json
-const CLI_VERSION = '0.0.1' // TODO: Import from package.json
-
-interface UpdateOptions {
-    cwd?: string
-}
-
-interface UpdateResult {
-    success: boolean
-    message: string
-    previousVersion?: string
-    newVersion?: string
-    cliOutdated?: boolean
-}
-
-/**
- * Compare two SemVer versions
- * Returns: -1 if a < b, 0 if a === b, 1 if a > b
- */
-function compareVersions(a: string, b: string): number {
-    const aParts = a.split('.').map(Number)
-    const bParts = b.split('.').map(Number)
-
-    for (let i = 0; i < 3; i++) {
-        const aNum = aParts[i] ?? 0
-        const bNum = bParts[i] ?? 0
-        if (aNum < bNum) return -1
-        if (aNum > bNum) return 1
-    }
-    return 0
-}
-
-/**
- * Update the Protocol to the latest version
- */
-export function update(options: UpdateOptions = {}): UpdateResult {
-    const cwd = options.cwd ?? process.cwd()
-
-    // Check if initialized
-    const autonomosDir = join(cwd, AUTONOMOS_DIR)
-    const manifestPath = join(autonomosDir, MANIFEST_FILE)
-
-    if (!existsSync(manifestPath)) {
-        return {
-            success: false,
-            message: 'Project not initialized. Run `autonomos init` first.',
-        }
-    }
-
-    // Read current manifest
-    const manifestContent = readFileSync(manifestPath, 'utf-8')
-    const manifest: Manifest = parseManifest(manifestContent)
-    const currentVersion = manifest.protocolVersion
-
-    // Compare versions
-    const comparison = compareVersions(currentVersion, PROTOCOL_VERSION)
-
-    if (comparison === 0) {
-        return {
-            success: true,
-            message: `Already up to date (Protocol v${PROTOCOL_VERSION})`,
-            previousVersion: currentVersion,
-            newVersion: PROTOCOL_VERSION,
-        }
-    }
-
-    if (comparison > 0) {
-        // Project uses a newer version than CLI knows
-        return {
-            success: false,
-            message: `This project uses Protocol v${currentVersion}, but your CLI only knows v${PROTOCOL_VERSION}. Update your CLI with \`npm i -g @autonomos/cli\`.`,
-            previousVersion: currentVersion,
-            newVersion: PROTOCOL_VERSION,
-            cliOutdated: true,
-        }
-    }
-
-    // Update Protocol (comparison < 0)
-    const protocolPath = join(autonomosDir, PROTOCOL_FILE)
-    writeFileSync(protocolPath, PROTOCOL_TEMPLATE)
-
-    // Update manifest
-    const updatedManifest: Manifest = {
-        ...manifest,
-        protocolVersion: PROTOCOL_VERSION,
-        cliVersion: CLI_VERSION,
-        lastUpdated: new Date().toISOString(),
-    }
-    writeFileSync(manifestPath, generateManifestContent(updatedManifest))
-
-    return {
-        success: true,
-        message: `Protocol updated: v${currentVersion} → v${PROTOCOL_VERSION}`,
-        previousVersion: currentVersion,
-        newVersion: PROTOCOL_VERSION,
-    }
-}

package/src/index.ts

@@ -1,205 +0,0 @@
-#!/usr/bin/env node
-import { Command } from 'commander'
-import pc from 'picocolors'
-
-import { PROTOCOL_VERSION } from '@autonomos/core'
-import { agents } from './commands/agents'
-import { init } from './commands/init'
-import { status } from './commands/status'
-import { update } from './commands/update'
-
-const CLI_VERSION = '0.0.1'
-
-const program = new Command()
-
-program
-    .name('autonomos')
-    .description(
-        pc.cyan(`CLI for the Autonomos Agent Protocol
-
-The Agent Protocol is a specification for AI agents to interact with codebases
-in a structured, consistent way. It defines how agents should read context,
-execute tasks, and persist knowledge.`) +
-            `
-
-Documentation: ${pc.underline('https://github.com/saoudi-h/autonomos')}`
-    )
-    .version(
-        `${pc.bold('CLI:')} ${pc.green(CLI_VERSION)}\n${pc.bold('Protocol:')} ${pc.green(PROTOCOL_VERSION)}`,
-        '-v, --version',
-        'Show version information'
-    )
-    .helpOption('-h, --help', 'Show help information')
-    .addHelpText(
-        'after',
-        `
-${pc.bold('Examples:')}
-  $ ${pc.cyan('autonomos init')}          Initialize the Agent Protocol in current directory
-  $ ${pc.cyan('autonomos update')}        Update Protocol to the latest version
-  $ ${pc.cyan('autonomos status')}        Show project status and task summary
-  $ ${pc.cyan('autonomos agents')}        List all AGENT.md files in the project
-
-${pc.bold('More info:')}
-  Run '${pc.cyan('autonomos <command> --help')}' for detailed information about a command.
-`
-    )
-
-program
-    .command('init')
-    .description('Initialize the Agent Protocol in the current directory')
-    .addHelpText(
-        'after',
-        `
-This command creates the following structure:
-  ${pc.blue('.autonomos/')}
-  ├── ${pc.white('manifest.json')}    # Protocol metadata and version
-  ├── ${pc.white('PROTOCOL.md')}      # Immutable protocol specification
-  ├── ${pc.white('TASKS.md')}         # Task registry
-  └── ${pc.blue('worklogs/')}        # Session logs directory
-  ${pc.white('AGENT.md')}             # Project context file (at root)
-
-${pc.bold('Examples:')}
-  $ ${pc.cyan('autonomos init')}
-  $ ${pc.cyan('cd my-project && autonomos init')}
-`
-    )
-    .option('-n, --dry-run', 'Preview what would be created without writing files')
-    .action(opts => {
-        const result = init({ dryRun: opts.dryRun })
-
-        if (!result.success) {
-            console.error(pc.red(`\n❌ ${result.message}`))
-            process.exit(1)
-        }
-
-        if (result.dryRun) {
-            console.log(pc.cyan(`\n🔍 ${result.message} (dry-run)`))
-        } else {
-            console.log(pc.green(`\n✅ ${result.message}`))
-        }
-
-        if (result.created.length > 0) {
-            console.log(`\n${pc.bold(result.dryRun ? 'Would create:' : 'Created:')}`)
-            result.created.forEach(file => console.log(`  ${pc.blue('📄')} ${pc.white(file)}`))
-        }
-
-        if (result.warnings.length > 0) {
-            console.log(pc.yellow('\nWarnings:'))
-            result.warnings.forEach(warn => console.log(`  ${pc.yellow('⚠️')}  ${warn}`))
-        }
-    })
-
-program
-    .command('update')
-    .description('Update the Protocol to the latest version')
-    .addHelpText(
-        'after',
-        `
-This command updates ${pc.white('PROTOCOL.md')} to the latest version embedded in the CLI.
-Only ${pc.white('PROTOCOL.md')} is modified; your ${pc.white('TASKS.md')} and ${pc.white('AGENT.md')} files are preserved.
-
-${pc.bold('Version comparison:')}
-  - If your project has an older version: Updates to the new version
-  - If your project has a newer version: Warns you to update the CLI
-  - If versions match: No action needed
-
-${pc.bold('Examples:')}
-  $ ${pc.cyan('autonomos update')}
-`
-    )
-    .action(() => {
-        const result = update()
-
-        if (!result.success) {
-            if (result.cliOutdated) {
-                console.error(pc.yellow(`\n⚠️  ${result.message}`))
-            } else {
-                console.error(pc.red(`\n❌ ${result.message}`))
-            }
-            process.exit(1)
-        }
-
-        console.log(pc.green(`\n✅ ${result.message}`))
-    })
-
-program
-    .command('status')
-    .description('Show project status and task summary')
-    .addHelpText(
-        'after',
-        `
-Displays information about the current project:
-  - Protocol version
-  - CLI version used for initialization
-  - Task summary (todo, in-progress, done, blocked)
-
-${pc.bold('Examples:')}
-  $ ${pc.cyan('autonomos status')}
-`
-    )
-    .action(() => {
-        const result = status()
-
-        if (!result.success) {
-            console.error(pc.red(`\n❌ ${result.message}`))
-            process.exit(1)
-        }
-
-        console.log(
-            `\n${pc.bold('📦 Protocol')} ${pc.green(`v${result.protocolVersion}`)} ${pc.dim(`(CLI v${result.cliVersion})`)}`
-        )
-
-        if (result.taskSummary) {
-            const s = result.taskSummary
-            console.log(`\n${pc.bold('📋 Tasks:')} ${pc.cyan(s.total)} total`)
-            console.log(`   ${pc.white('⬜ Todo:')} ${pc.white(s.todo)}`)
-            console.log(`   ${pc.blue('🔄 In Progress:')} ${pc.blue(s.inProgress)}`)
-            console.log(`   ${pc.green('✅ Done:')} ${pc.green(s.done)}`)
-            if (s.blocked > 0) {
-                console.log(`   ${pc.red('🚫 Blocked:')} ${pc.red(s.blocked)}`)
-            }
-        }
-    })
-
-program
-    .command('agents')
-    .description('List all AGENT.md files in the project')
-    .option('-a, --all', 'Search from project root instead of current directory')
-    .addHelpText(
-        'after',
-        `
-This command discovers and displays all ${pc.white('AGENT.md')} files in a tree structure.
-${pc.white('AGENT.md')} files provide context to AI agents about specific directories.
-
-${pc.bold('Modes:')}
-  (default)   Search from current directory downwards
-  --all       Search from project root (finds .autonomos or .git)
-
-${pc.bold('Examples:')}
-  $ ${pc.cyan('autonomos agents')}           # List from current directory
-  $ ${pc.cyan('autonomos agents --all')}     # List from project root
-  $ ${pc.cyan('cd packages/core && autonomos agents')}  # List only in packages/core
-`
-    )
-    .action(opts => {
-        const result = agents({ all: opts.all })
-
-        if (!result.success) {
-            console.error(pc.red(`\n❌ ${result.message}`))
-            process.exit(1)
-        }
-
-        console.log('\n' + (result.tree ?? result.message))
-        console.log(pc.dim(`\n${result.message}`))
-    })
-
-program
-    .command('version')
-    .description('Show the current Protocol version')
-    .action(() => {
-        console.log(
-            `${pc.bold('Agent Protocol')} ${pc.green(`v${PROTOCOL_VERSION}`)} ${pc.dim(`(CLI v${CLI_VERSION})`)}`
-        )
-    })
-
-program.parse()

package/tsconfig.json

@@ -1,36 +0,0 @@
-{
-    "extends": "@repo/tsconfig/base.json",
-    "compilerOptions": {
-        "target": "esnext",
-        "lib": ["es2022"],
-        "moduleDetection": "force",
-        "module": "esnext",
-        "moduleResolution": "bundler",
-        "resolveJsonModule": true,
-        "types": ["node", "vitest"],
-        "strict": true,
-        "noUnusedLocals": true,
-        "declaration": true,
-        "esModuleInterop": true,
-        "isolatedModules": true,
-        "verbatimModuleSyntax": true,
-        "skipLibCheck": true,
-        "baseUrl": ".",
-        "outDir": "./dist",
-        "rootDir": ".",
-        "paths": {
-            "@/*": ["src/*"],
-            "@tests/*": ["tests/*"]
-        }
-    },
-    "include": [
-        "./src/**/*",
-        "./src/**/*.json",
-        "tsdown.config.ts",
-        "vitest.config.ts",
-        "tests/**/*",
-        "lint-staged.config.mjs",
-        "prettier.config.mjs"
-    ],
-    "exclude": ["dist", "build", "node_modules", ".vscode", ".turbo", "coverage"]
-}

package/tsdown.config.ts

@@ -1,10 +0,0 @@
-import { base } from '@repo/tsdown'
-import type { UserConfigFn } from 'tsdown/config'
-import { defineConfig } from 'tsdown/config'
-
-const configFn: UserConfigFn = defineConfig(async options => ({
-    ...(await base(options, { ci: true })),
-    entry: ['./src/index.ts', './src/*/index.ts'],
-}))
-
-export default configFn

package/vitest.config.ts

@@ -1,9 +0,0 @@
-import { base } from '@repo/vitest'
-import type { ViteUserConfig } from 'vitest/config'
-import { defineConfig } from 'vitest/config'
-
-const config: ViteUserConfig = defineConfig({
-    ...base,
-})
-
-export default config