substrate-ai 0.1.10 → 0.1.12

package/README.md

@@ -1,5 +1,5 @@
 <p align="center">
-  <img src="https://github.com/user-attachments/assets/622dd577-2814-4657-bb28-112ed272486d" alt="Substrate — Autonomous Software Development Pipeline" />
+  <img src="https://raw.githubusercontent.com/johnplanow/substrate/main/assets/substrate-header.png" alt="Substrate — Autonomous Software Development Pipeline" />
 </p>
 
 # Substrate

package/dist/cli/index.js

@@ -8,7 +8,7 @@ import { fileURLToPath } from "url";
 import { dirname, extname, isAbsolute, join, relative, resolve } from "path";
 import { access, mkdir, readFile, readdir, stat, writeFile } from "fs/promises";
 import { execFile } from "child_process";
-import { existsSync, mkdirSync, readFileSync, readdirSync, realpathSync, renameSync, statSync, unlinkSync, writeFileSync } from "fs";
+import { cpSync, existsSync, mkdirSync, readFileSync, readdirSync, realpathSync, renameSync, statSync, unlinkSync, writeFileSync } from "fs";
 import yaml, { dump, load } from "js-yaml";
 import { z } from "zod";
 import { fileURLToPath as fileURLToPath$1 } from "node:url";
@@ -323,9 +323,9 @@ const DEFAULT_CONFIG = {
 
 //#endregion
 //#region src/cli/commands/templates.ts
-const __filename = fileURLToPath$1(import.meta.url);
-const __dirname = dirname$1(__filename);
-const TEMPLATES_DIR = join$1(__dirname, "..", "templates");
+const __filename$1 = fileURLToPath$1(import.meta.url);
+const __dirname$1 = dirname$1(__filename$1);
+const TEMPLATES_DIR = join$1(__dirname$1, "..", "templates");
 /**
 * Get the absolute path to a template YAML file.
 *
@@ -12114,6 +12114,15 @@ Analyze thoroughly and return ONLY the JSON array with no additional text.`;
 
 //#endregion
 //#region src/cli/commands/auto.ts
+const __filename = fileURLToPath$1(import.meta.url);
+const __dirname = dirname(__filename);
+/**
+* Absolute path to the Substrate package root.
+*
+* In source:  src/cli/commands/ → 3 levels up = repo root
+* Post-build: dist/cli/commands/ → 3 levels up = dist parent = package root
+*/
+const PACKAGE_ROOT = join(__dirname, "..", "..", "..");
 const logger$3 = createLogger("auto-cmd");
 /** BMAD baseline token total for full pipeline comparison (analysis+planning+solutioning+implementation) */
 const BMAD_BASELINE_TOKENS_FULL = 56800;
@@ -12313,18 +12322,41 @@ function formatPipelineSummary(run, tokenSummary, decisionsCount, storiesCount,
 	return lines.join("\n");
 }
 async function runAutoInit(options) {
-	const { pack: packName, projectRoot, outputFormat } = options;
+	const { pack: packName, projectRoot, outputFormat, force = false } = options;
 	const packPath = join(projectRoot, "packs", packName);
 	const dbRoot = await resolveMainRepoRoot(projectRoot);
 	const dbDir = join(dbRoot, ".substrate");
 	const dbPath = join(dbDir, "substrate.db");
 	try {
+		const localManifest = join(packPath, "manifest.yaml");
+		let scaffolded = false;
+		if (!existsSync(localManifest) || force) {
+			const bundledPackPath = join(PACKAGE_ROOT, "packs", packName);
+			if (!existsSync(join(bundledPackPath, "manifest.yaml"))) {
+				const errorMsg = `Pack '${packName}' not found locally or in bundled packs. Try reinstalling Substrate.`;
+				if (outputFormat === "json") process.stdout.write(formatOutput(null, "json", false, errorMsg) + "\n");
+				else process.stderr.write(`Error: ${errorMsg}\n`);
+				return 1;
+			}
+			if (force && existsSync(localManifest)) {
+				logger$3.info({ pack: packName }, "Replacing existing pack with bundled version");
+				process.stderr.write(`Warning: Replacing existing pack '${packName}' with bundled version\n`);
+			}
+			mkdirSync(dirname(packPath), { recursive: true });
+			cpSync(bundledPackPath, packPath, { recursive: true });
+			logger$3.info({
+				pack: packName,
+				dest: packPath
+			}, "Scaffolded methodology pack");
+			process.stdout.write(`Scaffolding methodology pack '${packName}' into packs/${packName}/\n`);
+			scaffolded = true;
+		}
 		const packLoader = createPackLoader();
 		try {
 			await packLoader.load(packPath);
 		} catch (err) {
 			const msg = err instanceof Error ? err.message : String(err);
-			const errorMsg = `Methodology pack '${packName}' not found. Run 'substrate auto init' first.\n${msg}`;
+			const errorMsg = `Methodology pack '${packName}' not found. Check that packs/${packName}/manifest.yaml exists or try reinstalling Substrate.\n${msg}`;
 			if (outputFormat === "json") process.stdout.write(formatOutput(null, "json", false, errorMsg) + "\n");
 			else process.stderr.write(`Error: ${errorMsg}\n`);
 			return 1;
@@ -12337,7 +12369,8 @@ async function runAutoInit(options) {
 		const successMsg = `Pack '${packName}' and database initialized successfully at ${dbPath}`;
 		if (outputFormat === "json") process.stdout.write(formatOutput({
 			pack: packName,
-			dbPath
+			dbPath,
+			scaffolded
 		}, "json", true) + "\n");
 		else process.stdout.write(`${successMsg}\n`);
 		return 0;
@@ -13479,12 +13512,13 @@ async function runAmendCommand(options) {
 */
 function registerAutoCommand(program, _version = "0.0.0", projectRoot = process.cwd()) {
 	const auto = program.command("auto").description("Autonomous implementation pipeline");
-	auto.command("init").description("Initialize a methodology pack and decision store for autonomous pipeline").option("--pack <name>", "Methodology pack name", "bmad").option("--project-root <path>", "Project root directory", projectRoot).option("--output-format <format>", "Output format: human (default) or json", "human").action(async (opts) => {
+	auto.command("init").description("Initialize a methodology pack and decision store for autonomous pipeline").option("--pack <name>", "Methodology pack name", "bmad").option("--project-root <path>", "Project root directory", projectRoot).option("--force", "Overwrite existing local pack with bundled version").option("--output-format <format>", "Output format: human (default) or json", "human").action(async (opts) => {
 		const outputFormat = opts.outputFormat === "json" ? "json" : "human";
 		const exitCode = await runAutoInit({
 			pack: opts.pack,
 			projectRoot: opts.projectRoot,
-			outputFormat
+			outputFormat,
+			force: opts.force ?? false
 		});
 		process.exitCode = exitCode;
 	});
@@ -14566,12 +14600,12 @@ const logger = createLogger("cli");
 /** Resolve the package.json path relative to this file */
 async function getPackageVersion() {
 	try {
-		const __filename$1 = fileURLToPath(import.meta.url);
-		const __dirname$1 = dirname(__filename$1);
+		const __filename$2 = fileURLToPath(import.meta.url);
+		const __dirname$2 = dirname(__filename$2);
 		const paths = [
-			resolve(__dirname$1, "../../package.json"),
-			resolve(__dirname$1, "../package.json"),
-			resolve(__dirname$1, "../../../package.json")
+			resolve(__dirname$2, "../../package.json"),
+			resolve(__dirname$2, "../package.json"),
+			resolve(__dirname$2, "../../../package.json")
 		];
 		for (const pkgPath of paths) try {
 			const content = await readFile(pkgPath, "utf-8");

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "substrate-ai",
-  "version": "0.1.10",
+  "version": "0.1.12",
   "description": "Substrate — multi-agent orchestration daemon for AI coding agents",
   "type": "module",
   "license": "MIT",
@@ -23,7 +23,6 @@
   "bin": {
     "substrate": "./dist/cli/index.js"
   },
-  "readme": "README.npm.md",
   "main": "./dist/index.js",
   "exports": {
     ".": {
@@ -41,12 +40,11 @@
     "dist/**/*.json",
     "dist/cli/templates",
     "packs",
-    "README.md",
-    "README.npm.md"
+    "README.md"
   ],
   "scripts": {
     "build": "tsdown",
-    "postbuild": "cp -r src/cli/templates dist/cli/templates && sed 's|assets/substrate-header.png|https://github.com/user-attachments/assets/622dd577-2814-4657-bb28-112ed272486d|' README.md > README.npm.md",
+    "postbuild": "cp -r src/cli/templates dist/cli/templates",
     "dev": "tsx watch src/cli/index.ts",
     "test": "vitest run --coverage",
     "test:watch": "vitest",

package/README.npm.md

@@ -1,206 +0,0 @@
-<p align="center">
-  <img src="https://github.com/user-attachments/assets/622dd577-2814-4657-bb28-112ed272486d" alt="Substrate — Autonomous Software Development Pipeline" />
-</p>
-
-# Substrate
-
-Autonomous software development pipeline powered by multi-agent orchestration. Substrate takes a project idea from concept through analysis, planning, architecture, implementation, and code review — coordinating CLI-based AI agents (Claude Code, Codex, Gemini CLI) to do the work.
-
-Substrate follows a modular monolith pattern running as a single Node.js process. The orchestrator never calls LLMs directly — all intelligent work is delegated to CLI agents running as child processes in isolated git worktrees. The autonomous pipeline compiles BMAD methodology workflows into token-efficient agent dispatches.
-
-## Prerequisites
-
-- **Node.js** 22.0.0 or later
-- **git** 2.20 or later
-- At least one supported AI CLI agent installed:
-  - [Claude Code](https://docs.anthropic.com/en/docs/claude-code) (`claude`)
-  - [Codex CLI](https://github.com/openai/codex) (`codex`)
-  - Gemini CLI (`gemini`)
-
-## Installation
-
-Install as a project dependency:
-
-```bash
-npm install substrate-ai
-```
-
-Or install globally:
-
-```bash
-npm install -g substrate-ai
-```
-
-Verify the installation:
-
-```bash
-npx substrate --version   # project install
-substrate --version        # global install
-```
-
-> Examples below use `[npx] substrate` — include `npx` for project installs, omit for global.
-
-## Quick Start
-
-### Autonomous Pipeline (recommended)
-
-Got an idea? Substrate can take it from concept to working code.
-
-1. **Brainstorm** — explore your idea with a multi-persona AI session:
-
-```bash
-[npx] substrate brainstorm
-```
-
-2. **Initialize the pipeline** — set up the methodology pack and decision store:
-
-```bash
-[npx] substrate auto init
-```
-
-3. **Run the full pipeline** — analysis, planning, solutioning, and implementation:
-
-```bash
-[npx] substrate auto run
-```
-
-Substrate walks through the entire software development lifecycle autonomously:
-- **Analysis** — generates a product brief from your brainstorm
-- **Planning** — creates a PRD with requirements
-- **Solutioning** — produces architecture, epics, and stories
-- **Implementation** — dispatches agents to build, test, and code-review each story
-
-You can start from any phase or resume an interrupted run:
-
-```bash
-[npx] substrate auto run --from solutioning   # Skip to a specific phase
-[npx] substrate auto resume                    # Pick up where you left off
-[npx] substrate auto status                    # Check pipeline progress
-```
-
-### Pick Up an Existing BMAD Project
-
-Already have a project with BMAD artifacts (vanilla BMAD or the Beads-based ai-toolkit)? Substrate can pick up the remaining implementation work. It reads one directory — `_bmad-output/` — and doesn't care which tool created it.
-
-**What Substrate needs from your project:**
-
-| File | Required? | Purpose |
-|------|-----------|---------|
-| `_bmad-output/planning-artifacts/epics.md` | Yes | Parsed into per-epic context shards |
-| `_bmad-output/planning-artifacts/architecture.md` | Yes | Tech stack and constraints for agents |
-| `_bmad-output/implementation-artifacts/*.md` | Optional | Existing story files — Substrate skips create-story for any it finds |
-| `package.json` | Optional | Test framework detection |
-
-**Three commands:**
-
-```bash
-npm install substrate-ai
-[npx] substrate auto init                          # Seeds context from _bmad-output/
-[npx] substrate auto run --stories 5-3,5-4,6-1    # Only the unfinished story keys
-```
-
-For each story, Substrate runs: **create-story** (skipped if story file exists) → **dev-story** (implement) → **code-review** (adversarial review). Non-conflicting stories run in parallel automatically.
-
-Substrate does not read `sprint-status.yaml` or `.beads/` — you decide what's left by choosing which story keys to pass.
-
-## Supported Agents
-
-| Agent ID | CLI Tool | Billing |
-|----------|----------|---------|
-| `claude-code` | Claude Code | Subscription (Max) or API key |
-| `codex` | Codex CLI | Subscription (ChatGPT Plus/Pro) or API key |
-| `gemini` | Gemini CLI | Subscription or API key |
-
-## Commands
-
-### Pipeline
-
-| Command | Description |
-|---------|-------------|
-| `substrate brainstorm` | Interactive multi-persona ideation session |
-| `substrate auto init` | Initialize methodology pack for autonomous pipeline |
-| `substrate auto run` | Run the full pipeline (analysis → implement) |
-| `substrate auto run --from <phase>` | Start from a specific phase |
-| `substrate auto resume` | Resume an interrupted pipeline run |
-| `substrate auto status` | Show pipeline run status |
-
-### Monitoring
-
-| Command | Description |
-|---------|-------------|
-| `substrate monitor status` | View task metrics and agent performance |
-| `substrate monitor report` | Generate a detailed performance report |
-| `substrate cost-report` | View cost and token usage summary |
-
-### Setup
-
-| Command | Description |
-|---------|-------------|
-| `substrate init` | Initialize project configuration |
-| `substrate --help` | Show all available commands |
-
-## Configuration
-
-Substrate reads configuration from `.substrate/config.yaml` in your project root. Run `[npx] substrate init` to generate a default config.
-
-## Development
-
-```bash
-# Clone and install
-git clone https://github.com/johnplanow/substrate.git
-cd substrate
-npm install
-
-# Build
-npm run build
-
-# Run tests
-npm test
-
-# Development mode (watch)
-npm run dev
-
-# Type check
-npm run typecheck
-
-# Lint
-npm run lint
-```
-
-## Manual Task Graphs
-
-For fine-grained control, you can define exactly what agents should do in a YAML task graph:
-
-```yaml
-version: "1"
-session:
-  name: "my-tasks"
-tasks:
-  write-tests:
-    name: "Write unit tests"
-    prompt: |
-      Look at the src/utils/ directory.
-      Write comprehensive unit tests for all exported functions.
-    type: testing
-    agent: claude-code
-  update-docs:
-    name: "Update README"
-    prompt: |
-      Read the README.md and verify it accurately describes
-      the project. Fix any inaccuracies.
-    type: docs
-    agent: codex
-    depends_on:
-      - write-tests
-```
-
-```bash
-[npx] substrate start --graph tasks.yaml              # Execute the graph
-[npx] substrate plan --graph tasks.yaml               # Preview without running
-```
-
-Tasks without dependencies run in parallel. Each agent gets its own isolated git worktree.
-
-## License
-
-MIT