@nexus-cortex/cli 4.33.0 → 4.34.1

package/docs/user-guide.md

@@ -1,291 +0,0 @@
-# Nexus Cortex — User Guide
-
-The full headless workflow: the `cortex` CLI, the HTTP agent server, the REST API, sessions,
-PR review, deployment, and troubleshooting. For setup see the [README](../README.md); for
-internals see [Architecture](architecture.md).
-
-## Install
-
-The simplest install is the `nexus-cortex` meta-package — it pulls in the `cortex` CLI and the
-HTTP server together:
-
-```bash
-npm install -g nexus-cortex
-```
-
-Prefer to install the components yourself? They're published individually:
-
-```bash
-npm install -g @nexus-cortex/cli @nexus-cortex/server
-```
-
-From source (`npm run build` auto-links the global commands):
-
-```bash
-npm install && npm run build     # multi-pass build, then links `cortex`
-npm run link                     # re-link any time (self-healing)
-```
-
-### Embed the library
-
-To drive the orchestrator in your own code instead of through the CLI:
-
-```bash
-npm install @nexus-cortex/core @nexus-cortex/executors
-```
-```typescript
-import { CortexOrchestrator } from '@nexus-cortex/core';
-
-const cortex = new CortexOrchestrator({
-  modelId: 'claude-sonnet-4-6',
-  projectPath: process.cwd(),
-});
-const res = await cortex.processMessage({ role: 'user', content: 'Analyze this codebase' });
-```
-
-## The `cortex` CLI
-
-`cortex` is a headless command — one-shot or multi-turn natural-language queries, plus a
-full structured command set. The first query **auto-starts a local server**; it persists in
-the background and subsequent calls share one stateful session.
-
-```bash
-# Simple query
-cortex "What is this project?"
-
-# Specific model
-cortex --model deepseek-v4-flash "Explain TypeScript generics"
-
-# Multi-turn (session persists automatically)
-cortex "Remember the launch code is FALCON-42"
-cortex "What was the launch code?"
-
-# JSON output for scripting and agent workflows
-cortex --json "List the npm scripts" | jq '.content[0].text'
-
-# Session management
-cortex --sessions                          # List all sessions
-cortex --stats                             # Current session stats
-cortex --new "Start a fresh conversation"  # New session
-cortex --resume SESSION_ID "Continue here" # Resume a specific session
-cortex --quiet "Just the answer"           # Response only, no metadata
-```
-
-### Autonomous agent (one-shot)
-
-`cortex agent` (alias `cortex run`) runs one task to completion and exits — fresh session,
-auto-approves tools (headless has no interactive approver), self-stops the server on idle.
-Point it at a throwaway/worktree/sandbox dir on a real repo.
-
-```bash
-cortex agent "summarize the test gaps in this repo"
-cortex agent --cwd ./feature-branch "add a --version flag and run the tests"
-cortex run --json "fix the failing lint" | jq '.toolUses[].name'
-```
-
-### Command groups
-
-Run `cortex --help`, or `cortex <group> --help` for any group:
-
-| Group | What it does |
-|-------|--------------|
-| `cortex "<prompt>"` | One-shot query (`-m/--model`, `--system`, `--max-tokens`, `--json`) |
-| `cortex agent` / `run` | Autonomous one-shot agent (`--cwd`, `--json`) |
-| `models` | `list` / `info` / `search` / `compare` / `cost` / `providers` / `switch` |
-| `sessions` | `list` / `view` / `export` / `resume` / `checkpoints` / `stats` / `search` / `compact` |
-| `config` | `get` / `set` / `categories` / `category` / `reset` |
-| `mcp` | `list` / `status` / `tools` / `enable` / `disable` / `init` / `validate` / `edit` |
-| `permissions` | `mode` / `set` / `grant` / `revoke` / `policies` / `tools` / `auto-approve` |
-| `autoresearch` | `bench` / `experiment` / `evaluate` / `fix` / `list` |
-| `context` | `status` / `compact` / `boundaries` / `strategy` / `savings` |
-| `middleware` | `list` / `status` / `enable` / `disable` / `config` |
-| `artifact` | `list` / `status` / `restart` / `stop` |
-| `tmux` | `list` |
-| `tools` | `list` / `info` |
-| `cache` | `metrics` |
-| `system-messages` | `list` / `view` / `reload` |
-| `server` | `status` / `start` |
-
-### Agent team usage
-
-The session ID enables multi-turn agent workflows:
-
-```bash
-SESSION=$(cortex --quiet --json "Analyze test gaps" | jq -r '.sessionId')
-cortex --resume $SESSION "Now fix the top priority gap"
-cortex --resume $SESSION "Run the tests to verify"
-```
-
-> **Interactive terminal UIs — Release 2.** A React/Ink chat UI (`neoncortex`), a Chalk UI
-> (`fuzzycortex`), the slash-command set, and a color-theme system ship in `@nexus-cortex/tui`
-> in the next release. Release 1 is headless-only.
-
-## Running the HTTP server
-
-The server is a **stateful agent** — sequential requests share one persistent session with
-full conversation history, tool execution, and context management. No terminal UI required.
-
-```bash
-# Production (uses DEFAULT_MODEL_ID from .env)
-cortex-server &
-# or, from source:
-node packages/server/dist/index.js &
-
-# Override model at launch
-DEFAULT_MODEL_ID=grok-4-1-fast-reasoning cortex-server &
-
-# Dev mode (auto-restart on code changes, auto-resumes session)
-cd packages/server && npm run dev
-```
-
-Port 4000 = API server. The HTML dashboard (sandbox/tmux viewer, port 4001) is opt-in: set
-`ENABLE_DASHBOARD=true` — a master switch, so when off no second port is ever bound.
-
-### Direct HTTP (curl)
-
-```bash
-# Send a message
-curl -s http://localhost:4000/v1/messages \
-  -H "Content-Type: application/json" \
-  -d '{"model":"grok-4-1-fast-reasoning","messages":[{"role":"user","content":"Read package.json and tell me the version"}]}'
-
-# Multi-turn: the next request continues the same conversation
-curl -s http://localhost:4000/v1/messages \
-  -H "Content-Type: application/json" \
-  -d '{"model":"grok-4-1-fast-reasoning","messages":[{"role":"user","content":"What dependencies does it have?"}]}'
-```
-
-### Response fields
-
-| Field | Description |
-|-------|-------------|
-| `content[]` | Model text response |
-| `toolUses[]` | Tools called (name, input, result) |
-| `usage.inputTokens` | Total input tokens (reveals system message overhead) |
-| `usage.outputTokens` | Response size |
-| `usage.cache` | Cache hit rate and cost savings |
-| `metadata.toolCallIterations` | Tool round-trips |
-
-### Session management API
-
-| Endpoint | Method | Description |
-|----------|--------|-------------|
-| `/sessions` | GET | List all sessions |
-| `/sessions/new` | POST | Start fresh session (old one saved) |
-| `/sessions/:id/stats` | GET | Token usage, turns, tool calls |
-| `/sessions/:id/messages` | GET | Full message history |
-| `/sessions/:id/model` | POST | Switch model mid-session |
-| `/sessions/:id/compaction` | POST | Trigger context compaction |
-| `/sessions/:id/cache/metrics` | GET | Cache hit rate and savings |
-| `/health` | GET | Server status and available models |
-
-Additional REST surfaces (run the server and `curl` them): `/tools`, `/permissions/*`,
-`/middleware/*`, `/config/*`, `/mcp/*`, `/system-messages/*`, and `/v1/approval-mode`.
-Session routes also include `export`, `DELETE`, `checkpoints`, `load`, `resume`, `context`,
-and `compaction/boundaries`.
-
-### PR review API
-
-When the git/PR tools are configured (see [Architecture → Permission System](architecture.md)):
-
-| Endpoint | Method | Description |
-|----------|--------|-------------|
-| `/v1/pr/review` | POST | Run a PR review pipeline (`{repo, prNumber, options?}`) |
-| `/v1/pr/create` | POST | Drive PR creation in an isolated worktree (`{repo, branch?, description?}`) |
-| `/v1/pr/list` | GET | List open PRs (`?repo=owner/repo`) |
-| `/v1/pr/webhook` | POST | GitHub webhook — requires `GITHUB_WEBHOOK_SECRET` + a valid `X-Hub-Signature-256` (returns 401 if no secret is set) |
-
-### Server lifecycle
-
-The server does **not** auto-shutdown after responses (unless `--idle-timeout` is set). Stop it explicitly:
-
-```bash
-pkill -f "packages/server/dist/index.js"   # or Ctrl+C if foreground
-```
-
-**Session resume**: by default the server starts a **fresh** session on boot. Opt into resuming:
-
-| Variable | Default | Behavior |
-|----------|---------|----------|
-| `AUTO_RESUME` | `false` | `true` → resume the most recent session on startup |
-| `RESUME_SESSION_ID` | — | Resume a specific session by UUID (overrides `AUTO_RESUME`) |
-
-With `AUTO_RESUME=true`, `tsx watch` restarts (dev mode) seamlessly continue your conversation —
-code changes take effect without losing session state. Pair it with `SERVER_IDLE_TIMEOUT` for a
-"sleep when idle, resume on wake" daemon.
-
-### Common launch variables
-
-| Variable | Default | Description |
-|----------|---------|-------------|
-| `DEFAULT_MODEL_ID` | `deepseek-v4-pro` | Model to use (any registry ID or alias) |
-| `PORT` | `4000` | Server port (falls back to the next free port if taken) |
-| `DEBUG` | `false` | Verbose logging (system messages, routes) |
-| `YOLO` | `false` | Auto-approve all tool executions (bypasses permissions) |
-| `CORTEX_MODE` | `persistent` | `stateless` for clean per-request sessions; `server` for HTTP-client mode |
-| `ENABLE_DASHBOARD` | `false` | Master switch for the sandbox/tmux web dashboard (binds `DASHBOARD_PORT`, default 4001) |
-
-Every variable is documented in [Configuration](configuration.md) and in `.env.example`. Run
-`cortex-server --help` for the server's own summary.
-
-## Development
-
-```bash
-npm run clean        # Clean build artifacts
-npm run build        # Build all packages (multi-pass; see Architecture)
-npm run typecheck    # Type checking
-npm test             # Run tests
-npm run test:ci      # Tests with coverage
-npm run lint         # Lint
-```
-
-### Dev workflow (stateful iteration)
-
-The recommended loop uses the server in dev mode with auto-resume:
-
-```bash
-# Terminal 1: server with hot reload
-cd packages/server && npm run dev
-
-# Terminal 2: send messages (each builds on the last)
-cortex "Read the orchestrator and explain the tool loop"
-cortex "Now add logging before each tool call"
-cortex "Run the tests to verify"
-```
-
-What survives restarts: **system-message edits** (read fresh each turn), **code changes**
-(tsx watch restarts + auto-resumes from JSONL), and **session state** (history, cache metrics,
-turn count restored from disk).
-
-## Production deployment
-
-```bash
-# Production server
-NODE_ENV=production PORT=4000 cortex-server
-
-# With PM2
-pm2 start packages/server/dist/index.js --name nexus-cortex
-```
-
-## Troubleshooting
-
-**Build errors** — clean and rebuild:
-```bash
-npm run clean && npm run build
-```
-
-**TypeScript errors** — `npm run typecheck`; ensure array accesses guard for `undefined`.
-
-**MCP server issues** — test the server manually and check config:
-```bash
-npx -y @modelcontextprotocol/server-filesystem /path/to/dir
-cat .cortex/mcp_config.json
-```
-
-**Missing API keys** — confirm the keys for the providers you use are set:
-```bash
-echo $ANTHROPIC_API_KEY
-```
-
-> `CORTEX.md` (project context) is generated on demand in your own project — run `/init` or
-> the `InitCortexContext` tool; it is not shipped with the package.