@codifier/cli 2.0.0

package/dist/cli/detect.js

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+/**
+ * Environment detection — identifies which LLM client is in use
+ * by checking for client-specific directories.
+ */
+import { existsSync } from 'fs';
+import { join } from 'path';
+export function detectEnvironment(cwd = process.cwd()) {
+    if (existsSync(join(cwd, '.claude'))) {
+        return {
+            clientType: 'claude-code',
+            commandsDir: join(cwd, '.claude', 'commands'),
+            mcpConfigPath: join(cwd, '.mcp.json'),
+        };
+    }
+    if (existsSync(join(cwd, '.cursor'))) {
+        return {
+            clientType: 'cursor',
+            commandsDir: join(cwd, '.cursor', 'rules'),
+            mcpConfigPath: join(cwd, '.cursor', 'mcp.json'),
+        };
+    }
+    if (existsSync(join(cwd, '.windsurf'))) {
+        return {
+            clientType: 'windsurf',
+            commandsDir: join(cwd, '.windsurf', 'commands'),
+            mcpConfigPath: join(cwd, '.windsurf', 'mcp.json'),
+        };
+    }
+    return {
+        clientType: 'generic',
+        commandsDir: join(cwd, '.codifier', 'commands'),
+        mcpConfigPath: join(cwd, '.codifier', 'mcp.json'),
+    };
+}
+//# sourceMappingURL=detect.js.map

package/dist/cli/detect.js.map

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package/dist/cli/doctor.d.ts

@@ -0,0 +1,5 @@
+/**
+ * `codifier doctor` — verify installation health.
+ */
+export declare function runDoctor(): Promise<void>;
+//# sourceMappingURL=doctor.d.ts.map

package/dist/cli/doctor.d.ts.map

@@ -0,0 +1 @@
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package/dist/cli/doctor.js

@@ -0,0 +1,58 @@
+/**
+ * `codifier doctor` — verify installation health.
+ */
+import { existsSync, readFileSync } from 'fs';
+import { join } from 'path';
+const REQUIRED_SKILLS = [
+    'initialize-project/SKILL.md',
+    'brownfield-onboard/SKILL.md',
+    'research-analyze/SKILL.md',
+];
+export async function runDoctor() {
+    const cwd = process.cwd();
+    const configPath = join(cwd, '.codifier', 'config.json');
+    let allGood = true;
+    console.log('\nCodifier Doctor\n');
+    // Check config
+    if (!existsSync(configPath)) {
+        console.error('✗ .codifier/config.json not found — run `codifier init` first');
+        allGood = false;
+    }
+    else {
+        console.log('✓ .codifier/config.json found');
+    }
+    // Check skill files
+    for (const skillFile of REQUIRED_SKILLS) {
+        const fullPath = join(cwd, '.codifier', 'skills', skillFile);
+        if (!existsSync(fullPath) || readFileSync(fullPath, 'utf8').trim().length === 0) {
+            console.error(`✗ Missing or empty: .codifier/skills/${skillFile}`);
+            allGood = false;
+        }
+        else {
+            console.log(`✓ .codifier/skills/${skillFile}`);
+        }
+    }
+    // Check MCP connectivity
+    if (existsSync(configPath)) {
+        try {
+            const config = JSON.parse(readFileSync(configPath, 'utf8'));
+            console.log('\nChecking MCP connectivity...');
+            const response = await fetch(`${config.serverUrl}/health`);
+            if (response.ok) {
+                console.log('✓ MCP server reachable');
+            }
+            else {
+                console.warn(`⚠ Health check returned ${response.status}`);
+                allGood = false;
+            }
+        }
+        catch {
+            console.warn('⚠ Could not reach MCP server');
+            allGood = false;
+        }
+    }
+    console.log(allGood ? '\n✅ All checks passed\n' : '\n⚠ Some checks failed — see above\n');
+    if (!allGood)
+        process.exit(1);
+}
+//# sourceMappingURL=doctor.js.map

package/dist/cli/doctor.js.map

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package/dist/cli/init.d.ts

@@ -0,0 +1,6 @@
+/**
+ * `codifier init` — one-time scaffolder.
+ * Copies skills, slash commands, and writes MCP config.
+ */
+export declare function runInit(): Promise<void>;
+//# sourceMappingURL=init.d.ts.map

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

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package/dist/cli/init.js

@@ -0,0 +1,93 @@
+/**
+ * `codifier init` — one-time scaffolder.
+ * Copies skills, slash commands, and writes MCP config.
+ */
+import { mkdirSync, cpSync, writeFileSync, existsSync } from 'fs';
+import { join, dirname } from 'path';
+import { fileURLToPath } from 'url';
+import * as readline from 'readline';
+import { detectEnvironment } from './detect.js';
+const __dirname = dirname(fileURLToPath(import.meta.url));
+// In the published npm package, skills/ is at the package root (sibling of dist/)
+// When running from dist/cli/, the package root is two levels up
+const PACKAGE_ROOT = join(__dirname, '..', '..');
+const SKILLS_SOURCE = join(PACKAGE_ROOT, 'skills');
+const COMMANDS_SOURCE = join(PACKAGE_ROOT, 'commands');
+function prompt(question) {
+    const rl = readline.createInterface({ input: process.stdin, output: process.stdout });
+    return new Promise((resolve) => {
+        rl.question(question, (answer) => {
+            rl.close();
+            resolve(answer.trim());
+        });
+    });
+}
+export async function runInit() {
+    const cwd = process.cwd();
+    const env = detectEnvironment(cwd);
+    console.log(`\nCodifier Init — detected client: ${env.clientType}\n`);
+    // 1. Create .codifier/skills/ and copy all skills
+    const skillsDest = join(cwd, '.codifier', 'skills');
+    mkdirSync(skillsDest, { recursive: true });
+    if (existsSync(SKILLS_SOURCE)) {
+        cpSync(SKILLS_SOURCE, skillsDest, { recursive: true });
+        console.log('✓ Skills copied to .codifier/skills/');
+    }
+    else {
+        console.warn(`⚠ Skills source not found at ${SKILLS_SOURCE} — skipping`);
+    }
+    // 2. Copy slash commands to client-specific location
+    mkdirSync(env.commandsDir, { recursive: true });
+    if (existsSync(COMMANDS_SOURCE)) {
+        cpSync(COMMANDS_SOURCE, env.commandsDir, { recursive: true });
+        console.log(`✓ Commands copied to ${env.commandsDir}`);
+    }
+    else {
+        console.warn(`⚠ Commands source not found at ${COMMANDS_SOURCE} — skipping`);
+    }
+    // 3. Prompt for server URL and API key
+    const serverUrl = await prompt('Codifier MCP server URL (e.g., https://codifier-mcp.fly.dev): ');
+    const apiKey = await prompt('Codifier API key: ');
+    // 4. Write .codifier/config.json
+    const configDir = join(cwd, '.codifier');
+    mkdirSync(configDir, { recursive: true });
+    const config = { serverUrl, apiKey, installedAt: new Date().toISOString() };
+    writeFileSync(join(configDir, 'config.json'), JSON.stringify(config, null, 2));
+    console.log('✓ Config saved to .codifier/config.json');
+    // 5. Write MCP config (client-specific format)
+    const mcpConfig = buildMcpConfig(serverUrl, apiKey);
+    writeFileSync(env.mcpConfigPath, JSON.stringify(mcpConfig, null, 2));
+    console.log(`✓ MCP config written to ${env.mcpConfigPath}`);
+    // 6. Verify connectivity (best-effort)
+    console.log('\nVerifying MCP connectivity...');
+    try {
+        const response = await fetch(`${serverUrl}/health`);
+        if (response.ok) {
+            console.log('✓ MCP server reachable');
+        }
+        else {
+            console.warn(`⚠ Health check returned ${response.status} — check your server URL`);
+        }
+    }
+    catch {
+        console.warn('⚠ Could not reach MCP server — check the URL and ensure the server is running');
+    }
+    // 7. Print summary
+    console.log('\n✅ Codifier installed successfully!\n');
+    console.log('Available skills:');
+    console.log('  • Initialize Project  →  /init');
+    console.log('  • Brownfield Onboard  →  /onboard');
+    console.log('  • Research & Analyze  →  /research');
+    console.log('\nRun /init in your LLM client to start your first project.\n');
+}
+function buildMcpConfig(serverUrl, apiKey) {
+    return {
+        mcpServers: {
+            codifier: {
+                url: `${serverUrl}/sse`,
+                headers: { Authorization: `Bearer ${apiKey}` },
+            },
+        },
+    };
+}
+//# sourceMappingURL=init.js.map

package/dist/cli/init.js.map

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package/dist/cli/update.d.ts

@@ -0,0 +1,5 @@
+/**
+ * `codifier update` — pull latest skills from the npm package.
+ */
+export declare function runUpdate(): Promise<void>;
+//# sourceMappingURL=update.d.ts.map

package/dist/cli/update.d.ts.map

@@ -0,0 +1 @@
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package/dist/cli/update.js

@@ -0,0 +1,25 @@
+/**
+ * `codifier update` — pull latest skills from the npm package.
+ */
+import { cpSync, existsSync } from 'fs';
+import { join, dirname } from 'path';
+import { fileURLToPath } from 'url';
+const __dirname = dirname(fileURLToPath(import.meta.url));
+const PACKAGE_ROOT = join(__dirname, '..', '..');
+const SKILLS_SOURCE = join(PACKAGE_ROOT, 'skills');
+export async function runUpdate() {
+    const cwd = process.cwd();
+    const skillsDest = join(cwd, '.codifier', 'skills');
+    if (!existsSync(skillsDest)) {
+        console.error('Error: .codifier/skills/ not found. Run `codifier init` first.');
+        process.exit(1);
+    }
+    if (!existsSync(SKILLS_SOURCE)) {
+        console.error(`Error: Skills source not found at ${SKILLS_SOURCE}`);
+        process.exit(1);
+    }
+    cpSync(SKILLS_SOURCE, skillsDest, { recursive: true });
+    console.log('✓ Skills updated in .codifier/skills/');
+    console.log('Note: .codifier/config.json was preserved.');
+}
+//# sourceMappingURL=update.js.map

package/dist/cli/update.js.map

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package/dist/index.js

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+/**
+ * CodifierMcp - MCP Server Entry Point
+ *
+ * Institutional memory system for AI-driven development.
+ * Provides fetch_context and update_memory tools via MCP protocol.
+ */
+import { getConfig } from './config/env.js';
+import { logger } from './utils/logger.js';
+import { createDataStore } from './datastore/factory.js';
+import { initializeMcpServer, connectStdioTransport } from './mcp/server.js';
+import { startHttpServer } from './http/server.js';
+/**
+ * Main entry point
+ */
+async function main() {
+    try {
+        logger.info('Starting CodifierMcp server');
+        // Load and validate configuration
+        const config = getConfig();
+        logger.info('Configuration loaded', {
+            dataStore: config.DATA_STORE,
+            transportMode: config.TRANSPORT_MODE,
+            httpPort: config.TRANSPORT_MODE === 'http' ? config.HTTP_PORT : undefined,
+            logLevel: config.LOG_LEVEL,
+        });
+        // Create data store instance via factory
+        const dataStore = createDataStore(config);
+        logger.debug('Data store instance created', { backend: config.DATA_STORE });
+        // Initialize MCP server (transport-agnostic)
+        const server = await initializeMcpServer({
+            name: 'codifier-mcp',
+            version: '0.1.0',
+            dataStore,
+        });
+        // Connect appropriate transport based on configuration
+        if (config.TRANSPORT_MODE === 'stdio') {
+            logger.info('Starting server in stdio mode');
+            await connectStdioTransport(server);
+            logger.info('CodifierMcp server is ready (stdio transport)');
+        }
+        else if (config.TRANSPORT_MODE === 'http') {
+            logger.info('Starting server in HTTP mode');
+            await startHttpServer(server, {
+                port: config.HTTP_PORT,
+                apiAuthToken: config.API_AUTH_TOKEN,
+                dataStore,
+            });
+            logger.info('CodifierMcp server is ready (HTTP transport)');
+        }
+        logger.info('Tools available: fetch_context, update_memory');
+        // Handle graceful shutdown
+        process.on('SIGINT', async () => {
+            logger.info('Received SIGINT, shutting down gracefully');
+            try {
+                await server.close();
+                logger.info('Server closed successfully');
+                process.exit(0);
+            }
+            catch (error) {
+                logger.error('Error during shutdown', error);
+                process.exit(1);
+            }
+        });
+        process.on('SIGTERM', async () => {
+            logger.info('Received SIGTERM, shutting down gracefully');
+            try {
+                await server.close();
+                logger.info('Server closed successfully');
+                process.exit(0);
+            }
+            catch (error) {
+                logger.error('Error during shutdown', error);
+                process.exit(1);
+            }
+        });
+    }
+    catch (error) {
+        logger.error('Fatal error during startup', {
+            error: error instanceof Error ? error.message : 'Unknown error',
+            stack: error instanceof Error ? error.stack : undefined,
+        });
+        process.exit(1);
+    }
+}
+// Start the server
+main();
+//# sourceMappingURL=index.js.map

package/package.json

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+{
+  "name": "@codifier/cli",
+  "version": "2.0.0",
+  "description": "MCP server for institutional memory management",
+  "main": "dist/index.js",
+  "bin": {
+    "codifier": "dist/cli/bin/codifier.js"
+  },
+  "type": "module",
+  "files": [
+    "dist/cli/",
+    "skills/",
+    "commands/"
+  ],
+  "scripts": {
+    "build": "tsc",
+    "dev": "tsc && node dist/index.js",
+    "watch": "tsc --watch",
+    "start": "node dist/index.js",
+    "test": "node --test tests/http-server.test.js",
+    "prepublishOnly": "npm run build"
+  },
+  "dependencies": {
+    "@modelcontextprotocol/sdk": "^1.21.1",
+    "@supabase/supabase-js": "^2.95.3",
+    "commander": "^14.0.3",
+    "cors": "^2.8.5",
+    "express": "^5.0.0",
+    "js-yaml": "^4.1.0",
+    "repomix": "^0.3.0",
+    "zod": "^3.23.8"
+  },
+  "devDependencies": {
+    "@types/cors": "^2.8.17",
+    "@types/express": "^5.0.0",
+    "@types/js-yaml": "^4.0.9",
+    "@types/node": "^20.12.7",
+    "typescript": "^5.5.3"
+  }
+}

package/skills/brownfield-onboard/SKILL.md

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+# Skill: Brownfield Onboard
+
+**Role:** Developer
+**Purpose:** Onboard existing codebases into the Codifier shared knowledge base by packing repositories, generating architectural summaries, and persisting learnings.
+
+See `../shared/codifier-tools.md` for full MCP tool reference.
+
+---
+
+## Prerequisites
+
+- Active MCP connection to the Codifier server
+- At least one repository URL (GitHub, GitLab, or local path)
+- A project to associate the snapshots with (existing or new)
+
+---
+
+## Workflow
+
+### Step 1 — Identify or Create the Project
+
+Call `manage_projects` with `operation: "list"` and show the user their existing projects.
+
+Ask: **"Which project should these repositories be associated with, or should we create a new one?"**
+
+- If **existing**: use the selected `project_id`.
+- If **new**: collect name and optionally org, then call `manage_projects` with `operation: "create"`.
+
+### Step 2 — Collect Repository URLs
+
+Ask the user to provide all repository URLs to onboard. They may provide:
+- One or more GitHub/GitLab/Bitbucket HTTPS URLs
+- Local filesystem paths (absolute)
+
+Ask: **"Are there any other repos to include, or is this the complete list?"**
+
+Also ask: **"What is the current state of these repos — active development, legacy, recently archived?"**
+
+### Step 3 — Fetch Existing Context
+
+Call `fetch_context` with `{ project_id }` to retrieve any prior memories for this project. Summarize relevant findings to the user — prior architectural decisions, existing rules, or previous onboarding notes are important context.
+
+### Step 4 — Pack Repositories
+
+For each repository URL:
+1. Call `pack_repo` with the URL, `project_id`, and a `version_label` (use current date: `"YYYY-MM"` or a tag like `"initial-onboard"`)
+2. Note the returned `repository_id`, `token_count`, and `file_count`
+3. Inform the user: "Packed `<repo-url>` — `<N>` files, `<M>` tokens"
+
+If a pack fails, log the error and continue with remaining repos.
+
+### Step 5 — Generate Architectural Summary
+
+Using the packed repository content (available in your context from the pack results) and any prior memories, generate a comprehensive architectural summary covering:
+
+1. **System Overview** — what the system does, its primary users, and its business purpose
+2. **Technology Stack** — languages, frameworks, databases, infrastructure
+3. **Module Structure** — major directories/packages and their responsibilities
+4. **Key Interfaces** — APIs, event buses, shared contracts between components
+5. **Data Flow** — how data moves through the system from input to output
+6. **External Dependencies** — third-party services, APIs, or systems integrated with
+7. **Known Issues / Technical Debt** — observations from the code (if apparent)
+8. **Conventions Observed** — naming patterns, file organisation, testing approach
+
+Present the summary to the user and ask: **"Does this accurately describe the system? What should be added or corrected?"**
+
+Incorporate feedback.
+
+### Step 6 — Persist Architectural Summary
+
+Call `update_memory`:
+```
+memory_type: "learning"
+title: "Architectural Summary — <repo-name or project-name>"
+content: { text: "<full summary markdown>", repos: ["<url1>", "<url2>"] }
+tags: ["architecture", "onboarding", "brownfield"]
+source_role: "developer"
+```
+
+### Step 7 — Persist Architectural Decisions
+
+For any significant architectural decisions uncovered (e.g., "uses event sourcing", "monorepo with Turborepo", "Postgres as primary store"), ask the user which to persist as formal documents.
+
+For each confirmed decision, call `update_memory`:
+```
+memory_type: "document"
+title: "ADR: <decision title>"
+content: { text: "<decision description, rationale, and consequences>" }
+tags: ["adr", "architecture"]
+source_role: "developer"
+```
+
+### Step 8 — Summarize
+
+Tell the user:
+- Project ID
+- Repositories packed (with IDs and token counts)
+- Memories persisted (IDs and titles)
+- How to retrieve this context in future: `fetch_context` with `{ project_id, tags: ["architecture"] }`
+
+---
+
+## Error Handling
+
+- If `pack_repo` times out or fails: note the error in the summary, ask the user if they want to retry or skip.
+- If a repo is private and credentials are not configured: inform the user that the server needs the relevant token (`GITHUB_TOKEN`, `GITLAB_TOKEN`) configured as an environment variable.
+- If the packed content is very large (>500K tokens): focus the architectural summary on the highest-level structural observations rather than deep code analysis.

package/skills/initialize-project/SKILL.md

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+# Skill: Initialize Project
+
+**Role:** Developer
+**Purpose:** Set up a new project in the Codifier shared knowledge base — collecting context, optionally packing repositories, and generating four key artifacts: Rules.md, Evals.md, Requirements.md, and Roadmap.md.
+
+See `../shared/codifier-tools.md` for full MCP tool reference.
+
+---
+
+## Prerequisites
+
+- Active MCP connection to the Codifier server
+- Project context: name, description, and optionally a Scope of Work (SOW) document and repo URLs
+
+---
+
+## Workflow
+
+Follow these steps conversationally. You are the state machine — call MCP tools only for data operations.
+
+### Step 1 — Identify or Create the Project
+
+Call `manage_projects` with `operation: "list"` to show the user their existing projects.
+
+Ask: **"Is this a new project, or do you want to use an existing one?"**
+
+- If **existing**: ask the user to select from the list; use that `project_id` for all subsequent calls.
+- If **new**: collect a project name and optionally an org name, then call `manage_projects` with `operation: "create"`. Use the returned `project_id` for all subsequent calls.
+
+### Step 2 — Collect Project Context
+
+Gather the following from the user in a single conversational turn:
+
+1. **Project name** (if not already set)
+2. **Description** — what does this project build and for whom?
+3. **Scope of Work (SOW)** — paste the SOW document, or describe key deliverables if no formal SOW exists
+4. **Repository URLs** (optional) — GitHub/GitLab URLs of codebases relevant to this project
+5. **Additional context** — any constraints, tech stack, team conventions, or prior decisions
+
+Confirm you have understood all provided context before proceeding.
+
+### Step 3 — Pack Repositories (if URLs provided)
+
+For each repository URL provided:
+1. Call `pack_repo` with the URL, `project_id`, and a `version_label` (use the current date or sprint label, e.g., `"2026-02"`)
+2. Note the returned `repository_id` and `token_count`
+3. Inform the user: "Packed `<repo-url>` — `<N>` tokens"
+
+If no URLs were provided, skip this step.
+
+### Step 4 — Fetch Existing Context
+
+Call `fetch_context` with `{ project_id }` (no type filter) to retrieve any prior memories for this project. This surfaces research findings, prior rules, or existing docs that should inform the new artifacts.
+
+Summarize any relevant findings to the user before generating artifacts.
+
+### Step 5 — Generate Rules.md
+
+Using the prompt template in `templates/rules-prompt.md`, generate a comprehensive set of development rules and coding standards for this project.
+
+**Substitute these placeholders with actual values:**
+- `{project_name}` — the project name
+- `{description}` — the project description
+- `{sow}` — the SOW or deliverables description
+- `{repo_urls}` — list of repo URLs (or "none provided")
+- `{additional_context}` — any extra context, including relevant memories from Step 4
+
+Present the generated Rules.md to the user inline. Ask: **"Does this look right? Any rules to add, remove, or change?"**
+
+Incorporate feedback before proceeding.
+
+### Step 6 — Generate Evals.md
+
+Using the prompt template in `templates/evals-prompt.md`, generate evaluation criteria from the confirmed Rules.md.
+
+**Substitute:**
+- `{rules}` — the confirmed Rules.md content
+- `{project_name}` — the project name
+- `{description}` — the project description
+
+Present Evals.md inline and ask for confirmation.
+
+### Step 7 — Generate Requirements.md
+
+Using the prompt template in `templates/requirements-prompt.md`, generate a detailed requirements document.
+
+**Substitute:**
+- `{project_name}`, `{description}`, `{sow}`, `{repo_urls}`, `{additional_context}`
+
+Present Requirements.md inline and ask for confirmation.
+
+### Step 8 — Generate Roadmap.md
+
+Using the prompt template in `templates/roadmap-prompt.md`, generate a phased implementation roadmap from Requirements.md.
+
+**Substitute:**
+- `{requirements}` — the confirmed Requirements.md content
+- `{project_name}`, `{description}`, `{repo_urls}`
+
+Present Roadmap.md inline and ask for confirmation.
+
+### Step 9 — Persist All Artifacts
+
+Call `update_memory` four times — once per artifact:
+
+| Artifact | `memory_type` | `title` | `source_role` |
+|----------|--------------|---------|---------------|
+| Rules.md | `document` | `"Rules.md — <project_name>"` | `"developer"` |
+| Evals.md | `document` | `"Evals.md — <project_name>"` | `"developer"` |
+| Requirements.md | `document` | `"Requirements.md — <project_name>"` | `"developer"` |
+| Roadmap.md | `document` | `"Roadmap.md — <project_name>"` | `"developer"` |
+
+For each call, set `content: { text: "<full artifact markdown>" }` and add relevant `tags` (e.g., `["rules", "standards"]` for Rules.md).
+
+### Step 10 — Summarize
+
+Tell the user:
+- Project ID (so they can reference it later)
+- Which artifacts were generated and persisted
+- How many MCP tool calls were made total
+- How to retrieve context in future sessions: `fetch_context` with `{ project_id, memory_type: "document" }`
+
+---
+
+## Context Assembly by Scenario
+
+### Greenfield + SOW
+Emphasize SOW deliverables and functional requirements in rules and requirements generation. The roadmap should sequence SOW milestones explicitly.
+
+### Greenfield — No SOW
+Prompt the user for key deliverables and target users before generating. Rules should be general-purpose but tailored to the tech stack described.
+
+### Brownfield + SOW
+Pack all repos first (Step 3). Fetch existing memories (Step 4) — prior rules and learnings are especially important. SOW delta (what's changing vs. what exists) should drive Requirements.md.
+
+### Brownfield — No SOW
+Pack all repos first. Spend extra time in conversation understanding the existing system before generating rules — ask about pain points, constraints, and what must not change.
+
+---
+
+## Error Handling
+
+- If `pack_repo` fails for a URL: log the error, inform the user, and continue with remaining URLs.
+- If `update_memory` fails: retry once. If still failing, present the artifact as a code block the user can save manually.
+- If the user provides no description or SOW: ask at least 3 clarifying questions before attempting artifact generation.