@nerviq/cli 1.8.5 → 1.8.7

package/README.md

@@ -1,362 +1,362 @@
-# Nerviq
-
-> Standardize and govern your AI coding agent setup — score, fix, and align across 8 platforms.
-
-[![npm version](https://img.shields.io/npm/v/@nerviq/cli)](https://www.npmjs.com/package/@nerviq/cli)
-[![License: AGPL-3.0](https://img.shields.io/badge/License-AGPL--3.0-blue.svg)](LICENSE)
-[![Checks: 2431](https://img.shields.io/badge/checks-2431-brightgreen)](https://github.com/nerviq/nerviq)
-
----
-
-### 8 Platforms Supported
-
-Nerviq audits, sets up, and governs AI coding agent configurations for **8 platforms**:
-
-| Platform | Checks | Status |
-|----------|--------|--------|
-| Claude Code | 393 | Full |
-| Codex (OpenAI) | 272 | Full |
-| Gemini CLI (Google) | 300 | Full |
-| GitHub Copilot | 299 | Full |
-| Cursor | 301 | Full |
-| Windsurf | 297 | Full |
-| Aider | 283 | Full |
-| OpenCode | 286 | Full |
-
-### 10 Stack-Specific Languages
-
-| Language | Checks | Key Areas |
-|----------|--------|-----------|
-| Python | 26 | pyproject, typing, pytest, linting, async, security |
-| Go | 21 | go.mod, vet, fmt, error wrapping, interfaces |
-| Rust | 21 | Cargo, clippy, unsafe docs, editions, cross-compile |
-| Java/Spring | 21 | Maven/Gradle, JUnit, Spring Boot, migrations |
-| Ruby | 16 | Gemfile, RSpec, Rubocop, Rails |
-| PHP | 16 | Composer, PHPUnit, Laravel, PSR |
-| .NET | 16 | csproj, NuGet, xUnit, EF Core |
-| Flutter | 15 | pubspec, analysis, state management, l10n |
-| Swift | 10 | SPM, SwiftLint, async/await, doc comments |
-| Kotlin | 10 | Gradle, ktlint, coroutines, Compose, KMP |
-
----
-
-## What Nerviq Does
-
-Nerviq scores your AI coding agent setup from 0 to 100, finds what's missing, and fixes it — with rollback for every change.
-
-```
-  nerviq audit
-  ═══════════════════════════════════════
-  Detected: React, TypeScript, Docker
-
-  ████████████████░░░░ 78/100
-
-  ✅ CLAUDE.md with architecture diagram
-  ✅ Hooks (PreToolUse + PostToolUse)
-  ✅ Custom skills (3 skills)
-  ✅ MCP servers configured
-
-  ⚡ Top 3 Next Actions
-     1. Add verification commands to CLAUDE.md
-     2. Configure deny rules for dangerous operations
-     3. Add path-specific rules in .claude/rules/
-
-  Next: nerviq setup
-```
-
-## Quick Start
-
-```bash
-npx @nerviq/cli audit              # Quick scan: score + top 3 actions
-npx @nerviq/cli audit --full       # Full audit with all checks + badge
-npx @nerviq/cli setup              # Generate starter-safe baseline
-npx @nerviq/cli augment            # Improvement plan, no writes
-npx @nerviq/cli governance         # Permission profiles + policy packs
-npx @nerviq/cli benchmark          # Before/after in isolated copy
-```
-
-No install required. Zero dependencies.
-
-## Get Started by Role
-
-| You are a... | Start here | Then |
-|--------------|------------|------|
-| **Solo developer** | `nerviq audit` → `nerviq augment` | `nerviq benchmark` |
-| **Team lead / DevEx** | `nerviq governance` → `nerviq audit --json` | CI threshold + `nerviq watch` |
-| **Enterprise / Platform** | `nerviq harmony-audit` → `nerviq harmony-drift` | Policy packs + `nerviq certify` |
-
-## 2,431 Checks Across 96 Categories (8 Platforms × ~300 Governance Rules)
-
-| Category Group | Checks | Examples |
-|----------------|--------|---------|
-| Stack-Specific (10 languages) | 172 | Python, Go, Rust, Java, Ruby, PHP, .NET, Flutter, Swift, Kotlin |
-| Platform Config & Instructions | ~150 | CLAUDE.md, AGENTS.md, rules, managed blocks |
-| Security & Trust | ~80 | permissions, deny rules, secrets, trust posture |
-| Quality & Testing | ~70 | verification loops, lint/test/build, coverage |
-| Automation & Hooks | ~60 | PreToolUse, PostToolUse, notification hooks |
-| Workflow & Commands | ~50 | skills, commands, agents, snapshots |
-| Git & Hygiene | ~40 | .gitignore, env protection, changelog |
-| Tools & MCP | ~40 | .mcp.json, multi-server, Context7 |
-| Governance & Compliance | ~30 | permission profiles, audit trails |
-| DevOps & Infrastructure | ~30 | Docker, CI, Terraform, monitoring |
-| Cross-Platform Intelligence | ~25 | harmony, synergy, drift detection |
-| Enterprise & Freshness | ~20 | freshness tracking, deprecation, SBOM |
-| Memory & Context | ~15 | context management, compaction, @path |
-| Prompting & Design | ~10 | XML tags, constraints, frontend patterns |
-
-## Harmony — Cross-Platform Alignment `GA`
-
-Harmony detects drift between your AI coding platforms and keeps them in sync.
-
-```bash
-npx @nerviq/cli harmony-audit      # Cross-platform DX audit (0-100 harmony score)
-npx @nerviq/cli harmony-sync       # Sync shared config across platforms
-npx @nerviq/cli harmony-drift      # Detect drift between platform configs
-npx @nerviq/cli harmony-advise     # Cross-platform improvement advice
-npx @nerviq/cli harmony-watch      # Live monitoring for config drift
-npx @nerviq/cli harmony-governance # Unified governance across platforms
-npx @nerviq/cli harmony-add <platform>  # Add a new platform to your project
-```
-
-## Synergy — Multi-Agent Amplification `EXPERIMENTAL`
-
-Synergy analyzes how your platforms work together and finds amplification opportunities. Currently uses static routing rules — learned routing is planned for v2.0.
-
-```bash
-npx @nerviq/cli synergy-report     # Multi-agent synergy analysis
-```
-
-Synergy evaluates compound audit results, discovers compensation patterns (where one platform covers another's gaps), and ranks recommendations by cross-platform impact.
-
-## SDK — `@nerviq/sdk` `BETA`
-
-Programmatic access to all Nerviq capabilities:
-
-```js
-const { audit, harmonyAudit, synergyReport, detectPlatforms } = require('@nerviq/sdk');
-
-const result = await audit('.', 'claude');
-console.log(`Score: ${result.score}/100`);
-
-const platforms = detectPlatforms('.');
-console.log(`Active platforms: ${platforms.join(', ')}`);
-
-const harmony = await harmonyAudit('.');
-console.log(`Harmony score: ${harmony.harmonyScore}/100`);
-```
-
-## MCP Server — `nerviq serve`
-
-Nerviq ships with a built-in MCP-compatible HTTP server for integration with AI agents:
-
-```bash
-npx @nerviq/cli serve --port 3000
-```
-
-Endpoints:
-- `GET /api/health` — Server health check
-- `GET /api/catalog` — Full check catalog
-- `POST /api/audit` — Run audit on a directory
-- `GET /api/harmony` — Cross-platform harmony data
-
-## Plugin System — `nerviq.config.js`
-
-Extend Nerviq with custom checks via a config file in your project root:
-
-```js
-// nerviq.config.js
-module.exports = {
-  plugins: [
-    {
-      name: 'my-company-checks',
-      checks: {
-        internalDocs: {
-          id: 'internalDocs',
-          name: 'Internal docs present',
-          check: (dir) => require('fs').existsSync(`${dir}/docs/internal.md`),
-          impact: 'medium',
-          category: 'Quality',
-          fix: 'Add docs/internal.md with team-specific guidelines',
-        },
-      },
-    },
-  ],
-};
-```
-
-See [docs/plugins.md](docs/plugins.md) for full plugin API reference.
-
-## GitHub Action
-
-Add Nerviq to your CI pipeline:
-
-```yaml
-# .github/workflows/nerviq.yml
-name: Nerviq Audit
-on: [push, pull_request]
-
-jobs:
-  audit:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: nerviq/nerviq@v1
-        with:
-          threshold: 60
-```
-
-The action outputs `score`, `passed`, and `total` for use in downstream steps. Fails the workflow if the score is below the configured threshold.
-
-## Certification
-
-Earn a Nerviq certification badge for your project:
-
-```bash
-npx @nerviq/cli certify            # Run certification and display badge
-```
-
-Levels:
-- **Gold** — Harmony score >= 80, all platforms >= 70
-- **Silver** — Harmony score >= 60, all platforms >= 50
-- **Bronze** — Any platform >= 40
-
-## All Commands
-
-| Command | What it does |
-|---------|-------------|
-| `nerviq audit` | Score 0-100 — quick scan with top 3 actions (default) |
-| `nerviq audit --full` | Full audit with all checks, weakest areas, confidence labels |
-| `nerviq fix <key>` | Auto-fix a specific check (shows score impact) |
-| `nerviq fix --all-critical` | Fix all critical issues at once |
-| `nerviq rollback` | Undo the most recent apply (delete created files) |
-| `nerviq rollback --list` | Show available rollback points |
-| `nerviq setup` | Generate starter-safe CLAUDE.md + hooks + commands |
-| `nerviq augment` | Repo-aware improvement plan (no writes) |
-| `nerviq suggest-only` | Structured report for sharing |
-| `nerviq plan` | Export proposal bundles with previews |
-| `nerviq apply` | Apply proposals with rollback |
-| `nerviq governance` | Permission profiles, hooks, policy packs |
-| `nerviq benchmark` | Before/after in isolated temp copy |
-| `nerviq check-health` | Detect regressions between audit snapshots |
-| `nerviq deep-review` | AI-powered config review (opt-in) |
-| `nerviq interactive` | Step-by-step guided wizard |
-| `nerviq watch` | Live monitoring with score delta |
-| `nerviq history` | Score history from snapshots |
-| `nerviq compare` | Compare latest vs previous |
-| `nerviq trend` | Export trend report |
-| `nerviq feedback` | Record recommendation outcomes |
-| `nerviq anti-patterns` | Detect anti-patterns in current project |
-| `nerviq freshness` | Show verification freshness for all checks |
-| `nerviq rules-export` | Export recommendation rules (human summary or --json) |
-| `nerviq badge` | shields.io badge for README |
-| `nerviq certify` | Certification level + badge |
-| `nerviq scan dir1 dir2` | Compare multiple repos |
-| `nerviq org scan dir1 dir2` | Aggregate multiple repos into one score table |
-| `nerviq harmony-audit` | Cross-platform DX audit |
-| `nerviq harmony-sync` | Sync config across platforms |
-| `nerviq harmony-drift` | Detect platform drift |
-| `nerviq harmony-advise` | Cross-platform advice |
-| `nerviq harmony-watch` | Live drift monitoring |
-| `nerviq harmony-governance` | Unified platform governance |
-| `nerviq synergy-report` | Multi-agent synergy analysis |
-| `nerviq catalog` | Show check catalog for all 8 platforms |
-| `nerviq doctor` | Self-diagnostics |
-| `nerviq convert` | Convert config between platforms |
-| `nerviq migrate` | Migrate platform config versions |
-| `nerviq serve` | Start local MCP-compatible HTTP API |
-
-## Options
-
-| Flag | Effect |
-|------|--------|
-| `--full` | Full audit output (all checks, weakest areas, confidence labels) |
-| `--verbose` | Full audit + medium-priority recommendations |
-| `--threshold N` | Exit 1 if score < N (for CI) |
-| `--json` | Machine-readable JSON output |
-| `--out FILE` | Write output to file |
-| `--snapshot` | Save audit snapshot for trending |
-| `--dry-run` | Preview changes without writing files |
-| `--config-only` | Only write config files, never source code |
-| `--auto` | Apply without prompts |
-| `--only A,B` | Limit apply to selected proposal IDs |
-| `--format sarif` | SARIF output for code scanning |
-| `--platform NAME` | Target platform (claude, codex, gemini, copilot, cursor, windsurf, aider, opencode) |
-| `--workspace GLOB` | Audit workspaces separately (e.g. packages/*) |
-| `--external PATH` | Benchmark an external repo |
-
-## Backed by Research
-
-Nerviq is built on the NERVIQ knowledge engine — the largest verified catalog of AI coding agent techniques:
-
-- **448+ research documents** covering all 8 platforms
-- **332+ experiments** with tested, rated results
-- **2,431 checks** across 8 platforms (~300 unique governance rules × 8 platform adaptations), each with `sourceUrl` and `confidence` level (0.0-1.0)
-- Every check is traceable to primary documentation or verified experiment
-- 90-day freshness cycle: stale findings are re-verified or pruned
-
-## Safety Modes
-
-Nerviq provides explicit safety controls so you decide what it can touch:
-
-| Mode | Flag | What it does |
-|------|------|-------------|
-| **Read-only** | `nerviq audit` | Reads files, writes nothing. Default command. |
-| **Suggest-only** | `nerviq suggest-only` | Generates markdown report, no file writes. |
-| **Dry-run** | `--dry-run` | Previews setup/fix/apply changes without writing. |
-| **Config-only** | `--config-only` | Only writes config files (.claude/, rules, hooks). Never touches source code. |
-| **Safe-write** | `--profile safe-write` | Default write profile. Creates new files, never overwrites existing ones. |
-| **Power-user** | `--profile power-user` | Overwrites existing files (use with `--snapshot` for rollback). |
-
-Every write command supports `--snapshot` for automatic backup before changes.
-
-## Privacy
-
-- **Zero dependencies** — nothing to audit
-- **Runs locally** — audit, setup, plan, apply, governance, benchmark all run on your machine
-- **Deep review is opt-in** — only `deep-review` sends selected config for AI analysis
-- **AGPL-3.0 Licensed** — open source
-
-## Links
-
-- **npm**: [@nerviq/cli](https://www.npmjs.com/package/@nerviq/cli)
-- **GitHub**: [github.com/nerviq/nerviq](https://github.com/nerviq/nerviq)
-- **Website**: [nerviq.net](https://nerviq.net)
-- **Discord**: [Join the community](https://discord.gg/nerviq)
-
----
-
-If Nerviq helped you, consider giving it a ⭐ on [GitHub](https://github.com/nerviq/nerviq) — it helps others discover the project.
-
-## What Nerviq Is — and Isn't
-
-**Best for:** Teams going from zero governance to a strong baseline — fast. If you're starting with AI coding agents or have a few platforms running without consistent configuration, Nerviq gets you to a governed setup quickly.
-
-**Not designed for:** Deeply customized setups with 20+ skills, agent teams, and bespoke MCP integrations. If you've already built advanced agent workflows, you may not need this.
-
-**Strongest at:** Agent configuration, workflow governance, repo policy hygiene, cross-platform alignment, and setup standardization.
-
-**Not a replacement for:** Deep architectural review of business logic, runtime performance profiling, or security penetration testing. Nerviq focuses on how your AI coding agents are configured and governed — not on what your application code does.
-
-**Confidence levels:** Every check includes a `confidence` score (0.0–1.0) and a `sourceUrl` linking to primary documentation. Checks marked `heuristic` are pattern-based and may produce false positives on non-standard project structures.
-
-**Feature maturity:**
-
-| Label | Meaning |
-|-------|---------|
-| `GA` | Stable, tested on real repos, safe for production use |
-| `BETA` | Works but has limited real-world testing. API may change |
-| `EXPERIMENTAL` | Early stage, static rules, results may vary |
-
-## Previously claudex-setup
-
-Nerviq was previously published as `claudex-setup`. If you were using it:
-
-```bash
-# Old
-npx claudex-setup
-
-# New
-npx @nerviq/cli audit
-```
-
-All features are preserved and expanded.
+# Nerviq
+
+> Standardize and govern your AI coding agent setup — score, fix, and align across 8 platforms.
+
+[![npm version](https://img.shields.io/npm/v/@nerviq/cli)](https://www.npmjs.com/package/@nerviq/cli)
+[![License: AGPL-3.0](https://img.shields.io/badge/License-AGPL--3.0-blue.svg)](LICENSE)
+[![Checks: 2431](https://img.shields.io/badge/checks-2431-brightgreen)](https://github.com/nerviq/nerviq)
+
+---
+
+### 8 Platforms Supported
+
+Nerviq audits, sets up, and governs AI coding agent configurations for **8 platforms**:
+
+| Platform | Checks | Status |
+|----------|--------|--------|
+| Claude Code | 393 | Full |
+| Codex (OpenAI) | 272 | Full |
+| Gemini CLI (Google) | 300 | Full |
+| GitHub Copilot | 299 | Full |
+| Cursor | 301 | Full |
+| Windsurf | 297 | Full |
+| Aider | 283 | Full |
+| OpenCode | 286 | Full |
+
+### 10 Stack-Specific Languages
+
+| Language | Checks | Key Areas |
+|----------|--------|-----------|
+| Python | 26 | pyproject, typing, pytest, linting, async, security |
+| Go | 21 | go.mod, vet, fmt, error wrapping, interfaces |
+| Rust | 21 | Cargo, clippy, unsafe docs, editions, cross-compile |
+| Java/Spring | 21 | Maven/Gradle, JUnit, Spring Boot, migrations |
+| Ruby | 16 | Gemfile, RSpec, Rubocop, Rails |
+| PHP | 16 | Composer, PHPUnit, Laravel, PSR |
+| .NET | 16 | csproj, NuGet, xUnit, EF Core |
+| Flutter | 15 | pubspec, analysis, state management, l10n |
+| Swift | 10 | SPM, SwiftLint, async/await, doc comments |
+| Kotlin | 10 | Gradle, ktlint, coroutines, Compose, KMP |
+
+---
+
+## What Nerviq Does
+
+Nerviq scores your AI coding agent setup from 0 to 100, finds what's missing, and fixes it — with rollback for every change.
+
+```
+  nerviq audit
+  ═══════════════════════════════════════
+  Detected: React, TypeScript, Docker
+
+  ████████████████░░░░ 78/100
+
+  ✅ CLAUDE.md with architecture diagram
+  ✅ Hooks (PreToolUse + PostToolUse)
+  ✅ Custom skills (3 skills)
+  ✅ MCP servers configured
+
+  ⚡ Top 3 Next Actions
+     1. Add verification commands to CLAUDE.md
+     2. Configure deny rules for dangerous operations
+     3. Add path-specific rules in .claude/rules/
+
+  Next: nerviq setup
+```
+
+## Quick Start
+
+```bash
+npx @nerviq/cli audit              # Quick scan: score + top 3 actions
+npx @nerviq/cli audit --full       # Full audit with all checks + badge
+npx @nerviq/cli setup              # Generate starter-safe baseline
+npx @nerviq/cli augment            # Improvement plan, no writes
+npx @nerviq/cli governance         # Permission profiles + policy packs
+npx @nerviq/cli benchmark          # Before/after in isolated copy
+```
+
+No install required. Zero dependencies.
+
+## Get Started by Role
+
+| You are a... | Start here | Then |
+|--------------|------------|------|
+| **Solo developer** | `nerviq audit` → `nerviq augment` | `nerviq benchmark` |
+| **Team lead / DevEx** | `nerviq governance` → `nerviq audit --json` | CI threshold + `nerviq watch` |
+| **Enterprise / Platform** | `nerviq harmony-audit` → `nerviq harmony-drift` | Policy packs + `nerviq certify` |
+
+## 2,431 Checks Across 96 Categories (8 Platforms × ~300 Governance Rules)
+
+| Category Group | Checks | Examples |
+|----------------|--------|---------|
+| Stack-Specific (10 languages) | 172 | Python, Go, Rust, Java, Ruby, PHP, .NET, Flutter, Swift, Kotlin |
+| Platform Config & Instructions | ~150 | CLAUDE.md, AGENTS.md, rules, managed blocks |
+| Security & Trust | ~80 | permissions, deny rules, secrets, trust posture |
+| Quality & Testing | ~70 | verification loops, lint/test/build, coverage |
+| Automation & Hooks | ~60 | PreToolUse, PostToolUse, notification hooks |
+| Workflow & Commands | ~50 | skills, commands, agents, snapshots |
+| Git & Hygiene | ~40 | .gitignore, env protection, changelog |
+| Tools & MCP | ~40 | .mcp.json, multi-server, Context7 |
+| Governance & Compliance | ~30 | permission profiles, audit trails |
+| DevOps & Infrastructure | ~30 | Docker, CI, Terraform, monitoring |
+| Cross-Platform Intelligence | ~25 | harmony, synergy, drift detection |
+| Enterprise & Freshness | ~20 | freshness tracking, deprecation, SBOM |
+| Memory & Context | ~15 | context management, compaction, @path |
+| Prompting & Design | ~10 | XML tags, constraints, frontend patterns |
+
+## Harmony — Cross-Platform Alignment `GA`
+
+Harmony detects drift between your AI coding platforms and keeps them in sync.
+
+```bash
+npx @nerviq/cli harmony-audit      # Cross-platform DX audit (0-100 harmony score)
+npx @nerviq/cli harmony-sync       # Sync shared config across platforms
+npx @nerviq/cli harmony-drift      # Detect drift between platform configs
+npx @nerviq/cli harmony-advise     # Cross-platform improvement advice
+npx @nerviq/cli harmony-watch      # Live monitoring for config drift
+npx @nerviq/cli harmony-governance # Unified governance across platforms
+npx @nerviq/cli harmony-add <platform>  # Add a new platform to your project
+```
+
+## Synergy — Multi-Agent Amplification `EXPERIMENTAL`
+
+Synergy analyzes how your platforms work together and finds amplification opportunities. Currently uses static routing rules — learned routing is planned for v2.0.
+
+```bash
+npx @nerviq/cli synergy-report     # Multi-agent synergy analysis
+```
+
+Synergy evaluates compound audit results, discovers compensation patterns (where one platform covers another's gaps), and ranks recommendations by cross-platform impact.
+
+## SDK — `@nerviq/sdk` `BETA`
+
+Programmatic access to all Nerviq capabilities:
+
+```js
+const { audit, harmonyAudit, synergyReport, detectPlatforms } = require('@nerviq/sdk');
+
+const result = await audit('.', 'claude');
+console.log(`Score: ${result.score}/100`);
+
+const platforms = detectPlatforms('.');
+console.log(`Active platforms: ${platforms.join(', ')}`);
+
+const harmony = await harmonyAudit('.');
+console.log(`Harmony score: ${harmony.harmonyScore}/100`);
+```
+
+## MCP Server — `nerviq serve`
+
+Nerviq ships with a built-in MCP-compatible HTTP server for integration with AI agents:
+
+```bash
+npx @nerviq/cli serve --port 3000
+```
+
+Endpoints:
+- `GET /api/health` — Server health check
+- `GET /api/catalog` — Full check catalog
+- `POST /api/audit` — Run audit on a directory
+- `GET /api/harmony` — Cross-platform harmony data
+
+## Plugin System — `nerviq.config.js`
+
+Extend Nerviq with custom checks via a config file in your project root:
+
+```js
+// nerviq.config.js
+module.exports = {
+  plugins: [
+    {
+      name: 'my-company-checks',
+      checks: {
+        internalDocs: {
+          id: 'internalDocs',
+          name: 'Internal docs present',
+          check: (dir) => require('fs').existsSync(`${dir}/docs/internal.md`),
+          impact: 'medium',
+          category: 'Quality',
+          fix: 'Add docs/internal.md with team-specific guidelines',
+        },
+      },
+    },
+  ],
+};
+```
+
+See [docs/plugins.md](docs/plugins.md) for full plugin API reference.
+
+## GitHub Action
+
+Add Nerviq to your CI pipeline:
+
+```yaml
+# .github/workflows/nerviq.yml
+name: Nerviq Audit
+on: [push, pull_request]
+
+jobs:
+  audit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: nerviq/nerviq@v1
+        with:
+          threshold: 60
+```
+
+The action outputs `score`, `passed`, and `total` for use in downstream steps. Fails the workflow if the score is below the configured threshold.
+
+## Certification
+
+Earn a Nerviq certification badge for your project:
+
+```bash
+npx @nerviq/cli certify            # Run certification and display badge
+```
+
+Levels:
+- **Gold** — Harmony score >= 80, all platforms >= 70
+- **Silver** — Harmony score >= 60, all platforms >= 50
+- **Bronze** — Any platform >= 40
+
+## All Commands
+
+| Command | What it does |
+|---------|-------------|
+| `nerviq audit` | Score 0-100 — quick scan with top 3 actions (default) |
+| `nerviq audit --full` | Full audit with all checks, weakest areas, confidence labels |
+| `nerviq fix <key>` | Auto-fix a specific check (shows score impact) |
+| `nerviq fix --all-critical` | Fix all critical issues at once |
+| `nerviq rollback` | Undo the most recent apply (delete created files) |
+| `nerviq rollback --list` | Show available rollback points |
+| `nerviq setup` | Generate starter-safe CLAUDE.md + hooks + commands |
+| `nerviq augment` | Repo-aware improvement plan (no writes) |
+| `nerviq suggest-only` | Structured report for sharing |
+| `nerviq plan` | Export proposal bundles with previews |
+| `nerviq apply` | Apply proposals with rollback |
+| `nerviq governance` | Permission profiles, hooks, policy packs |
+| `nerviq benchmark` | Before/after in isolated temp copy |
+| `nerviq check-health` | Detect regressions between audit snapshots |
+| `nerviq deep-review` | AI-powered config review (opt-in) |
+| `nerviq interactive` | Step-by-step guided wizard |
+| `nerviq watch` | Live monitoring with score delta |
+| `nerviq history` | Score history from snapshots |
+| `nerviq compare` | Compare latest vs previous |
+| `nerviq trend` | Export trend report |
+| `nerviq feedback` | Record recommendation outcomes |
+| `nerviq anti-patterns` | Detect anti-patterns in current project |
+| `nerviq freshness` | Show verification freshness for all checks |
+| `nerviq rules-export` | Export recommendation rules (human summary or --json) |
+| `nerviq badge` | shields.io badge for README |
+| `nerviq certify` | Certification level + badge |
+| `nerviq scan dir1 dir2` | Compare multiple repos |
+| `nerviq org scan dir1 dir2` | Aggregate multiple repos into one score table |
+| `nerviq harmony-audit` | Cross-platform DX audit |
+| `nerviq harmony-sync` | Sync config across platforms |
+| `nerviq harmony-drift` | Detect platform drift |
+| `nerviq harmony-advise` | Cross-platform advice |
+| `nerviq harmony-watch` | Live drift monitoring |
+| `nerviq harmony-governance` | Unified platform governance |
+| `nerviq synergy-report` | Multi-agent synergy analysis |
+| `nerviq catalog` | Show check catalog for all 8 platforms |
+| `nerviq doctor` | Self-diagnostics |
+| `nerviq convert` | Convert config between platforms |
+| `nerviq migrate` | Migrate platform config versions |
+| `nerviq serve` | Start local MCP-compatible HTTP API |
+
+## Options
+
+| Flag | Effect |
+|------|--------|
+| `--full` | Full audit output (all checks, weakest areas, confidence labels) |
+| `--verbose` | Full audit + medium-priority recommendations |
+| `--threshold N` | Exit 1 if score < N (for CI) |
+| `--json` | Machine-readable JSON output |
+| `--out FILE` | Write output to file |
+| `--snapshot` | Save audit snapshot for trending |
+| `--dry-run` | Preview changes without writing files |
+| `--config-only` | Only write config files, never source code |
+| `--auto` | Apply without prompts |
+| `--only A,B` | Limit apply to selected proposal IDs |
+| `--format sarif` | SARIF output for code scanning |
+| `--platform NAME` | Target platform (claude, codex, gemini, copilot, cursor, windsurf, aider, opencode) |
+| `--workspace GLOB` | Audit workspaces separately (e.g. packages/*) |
+| `--external PATH` | Benchmark an external repo |
+
+## Backed by Research
+
+Nerviq is built on the NERVIQ knowledge engine — the largest verified catalog of AI coding agent techniques:
+
+- **448+ research documents** covering all 8 platforms
+- **332+ experiments** with tested, rated results
+- **2,431 checks** across 8 platforms (~300 unique governance rules × 8 platform adaptations), each with `sourceUrl` and `confidence` level (0.0-1.0)
+- Every check is traceable to primary documentation or verified experiment
+- 90-day freshness cycle: stale findings are re-verified or pruned
+
+## Safety Modes
+
+Nerviq provides explicit safety controls so you decide what it can touch:
+
+| Mode | Flag | What it does |
+|------|------|-------------|
+| **Read-only** | `nerviq audit` | Reads files, writes nothing. Default command. |
+| **Suggest-only** | `nerviq suggest-only` | Generates markdown report, no file writes. |
+| **Dry-run** | `--dry-run` | Previews setup/fix/apply changes without writing. |
+| **Config-only** | `--config-only` | Only writes config files (.claude/, rules, hooks). Never touches source code. |
+| **Safe-write** | `--profile safe-write` | Default write profile. Creates new files, never overwrites existing ones. |
+| **Power-user** | `--profile power-user` | Overwrites existing files (use with `--snapshot` for rollback). |
+
+Every write command supports `--snapshot` for automatic backup before changes.
+
+## Privacy
+
+- **Zero dependencies** — nothing to audit
+- **Runs locally** — audit, setup, plan, apply, governance, benchmark all run on your machine
+- **Deep review is opt-in** — only `deep-review` sends selected config for AI analysis
+- **AGPL-3.0 Licensed** — open source
+
+## Links
+
+- **npm**: [@nerviq/cli](https://www.npmjs.com/package/@nerviq/cli)
+- **GitHub**: [github.com/nerviq/nerviq](https://github.com/nerviq/nerviq)
+- **Website**: [nerviq.net](https://nerviq.net)
+- **Discord**: [Join the community](https://discord.gg/nerviq)
+
+---
+
+If Nerviq helped you, consider giving it a ⭐ on [GitHub](https://github.com/nerviq/nerviq) — it helps others discover the project.
+
+## What Nerviq Is — and Isn't
+
+**Best for:** Teams going from zero governance to a strong baseline — fast. If you're starting with AI coding agents or have a few platforms running without consistent configuration, Nerviq gets you to a governed setup quickly.
+
+**Not designed for:** Deeply customized setups with 20+ skills, agent teams, and bespoke MCP integrations. If you've already built advanced agent workflows, you may not need this.
+
+**Strongest at:** Agent configuration, workflow governance, repo policy hygiene, cross-platform alignment, and setup standardization.
+
+**Not a replacement for:** Deep architectural review of business logic, runtime performance profiling, or security penetration testing. Nerviq focuses on how your AI coding agents are configured and governed — not on what your application code does.
+
+**Confidence levels:** Every check includes a `confidence` score (0.0–1.0) and a `sourceUrl` linking to primary documentation. Checks marked `heuristic` are pattern-based and may produce false positives on non-standard project structures.
+
+**Feature maturity:**
+
+| Label | Meaning |
+|-------|---------|
+| `GA` | Stable, tested on real repos, safe for production use |
+| `BETA` | Works but has limited real-world testing. API may change |
+| `EXPERIMENTAL` | Early stage, static rules, results may vary |
+
+## Previously nerviq-cli
+
+Nerviq was previously published as `nerviq-cli`. If you were using it:
+
+```bash
+# Old
+npx nerviq-cli
+
+# New
+npx @nerviq/cli audit
+```
+
+All features are preserved and expanded.