Dotai CLI

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AI coding tools each expect their own config directory — .claude/, .gemini/, .github/, .agents/. dotai creates a single .ai/ directory as your source of truth and symlinks everything to where each tool expects it.

Edit one file. Every tool stays in sync.

What's New in v3.1.0 — Resource Management Commands

Manage every aspect of your AI tool configuration from the CLI — MCP servers, skills, rules, slash commands, and config settings.

dotai mcp add my-server -c npx -a "my-pkg,serve,--stdio"   # add MCP server
dotai skill add code-review -d "Code review guidelines"    # add skill
dotai rule add api-conventions --always                     # add rule
dotai cmd add deploy                                        # add slash command
dotai config show                                           # view config

All commands auto-sync across every enabled tool — Claude, Gemini, Antigravity, and Copilot.

Also includes

• Spec-Driven Development (SDD) — 8-phase workflow for spec-traced code generation
• AI-Driven Knowledge Base — dotai knowledge init scaffolds the KB + /learn command; agents populate it
• Built-in /git-stage-commit — Stage, generate commit message, and commit locally (no push)
• 4 AI Tools — Gemini CLI, Antigravity, Claude Code, GitHub Copilot

Why dotai?

Without dotai, you juggle:

CLAUDE.md            ← Claude Code reads this
GEMINI.md            ← Gemini CLI reads this
.github/copilot-instructions.md  ← Copilot reads this
.gemini/rules/       ← Antigravity reads this

With dotai:

.ai/AI.md  →  symlinked to all of the above

One file to write. Four tools that read it. Zero drift.

Quick Start

# Install globally
npm install -g @nbslabs/dotai

# Initialize in your project
cd your-project
dotai init

# That's it — your .ai/ folder is ready and symlinks are created

How It Works

.ai/                           Your source of truth (committed to git)
├── AI.md               ──→    CLAUDE.md, GEMINI.md, AGENTS.md,
│                               .github/copilot-instructions.md
├── DOTAI.md                   Quick reference guide (this explains your setup)
├── rules/              ──→    .claude/rules/, .gemini/rules/,
│                               .agents/rules/
├── commands/           ──→    .claude/commands/
├── commands-gemini/    ──→    .gemini/commands/ (Gemini uses .toml format)
├── skills/             ──→    .claude/skills/, .gemini/skills/,
│                               .agents/skills/, .github/skills/
├── workflows/          ──→    .agents/workflows/
├── knowledge/          ──→    .claude/knowledge/, .gemini/knowledge/, .github/knowledge/
├── settings/
│   ├── claude.json     ──→    .claude/settings.json
│   └── gemini.json     ──→    .gemini/settings.json
└── ignore/
    └── .aiignore       ──→    .geminiignore

Commands

Core Commands

Command	Description
dotai init	Scaffold .ai/ directory, or restore from existing .dotai.json
dotai link [tools...]	Create symlinks for specified or all configured tools
dotai unlink [tools...]	Remove symlinks, optionally restore backed-up originals
dotai status	Show the current state of every symlink
dotai add <tool>	Add a new tool to an existing project
dotai remove <tool>	Remove a tool and clean up its symlinks
dotai list	List all supported tools and their link status
dotai sync	Re-evaluate and repair all symlinks
dotai doctor	Run diagnostics and auto-fix issues
dotai upgrade	Update .ai/ scaffold files to latest templates

Resource Management (v3.1.0)

Command	Description
dotai mcp add <name>	Add an MCP server to all enabled tool settings
dotai mcp remove <name>	Remove an MCP server from all settings files
dotai mcp list	List all configured MCP servers across tools
dotai skill add <name>	Create a skill package with SKILL.md template
dotai skill remove <name>	Delete a skill package
dotai skill list	List all skills with descriptions and tool linkage
dotai rule add <name>	Create a coding rule file with frontmatter
dotai rule remove <name>	Delete a rule file
dotai rule list	List all rules with alwaysApply status
dotai cmd add <name>	Create a slash command across all enabled tool formats
dotai cmd remove <name>	Remove a command from all formats
dotai cmd list	List all commands merged across tool formats
dotai config get <key>	Read a config value from .dotai.json
dotai config set <key> <value>	Set a config value
dotai config show	Display full configuration

SDD (Spec-Driven Development)

Command	Description
dotai sdd init	Scaffold SDD toolkit (skills, commands, templates)
dotai sdd new <name>	Create a new feature directory from template
dotai sdd remove <name>	Remove a feature and all its artifacts
dotai sdd list	List all features and their current phase
dotai sdd status [name]	Show detailed phase progress for a feature

Supported Tools

ID	Tool	Native Dir	What Gets Symlinked
claude	Claude Code	.claude/	AI.md, settings, commands, skills, knowledge
gemini	Gemini CLI	.gemini/	AI.md, settings, commands (.toml), skills, ignore, knowledge
copilot	GitHub Copilot	.github/	AI.md, prompts, instructions, skills, knowledge
antigravity	Antigravity	.gemini/	AI.md, AGENTS.md, settings, rules, workflows, skills, knowledge

Knowledge Base

dotai knowledge creates a persistent codebase memory layer at .ai/knowledge/ and equips your AI agents with the skills and commands to populate it.

Quick Start

dotai knowledge init   # scaffold knowledge dir + install /learn command

Then ask your AI agent:

/learn

The /learn command instructs the agent to deeply analyze your codebase and persist findings (architecture, patterns, gotchas) into .ai/knowledge/.

How It Works

1. dotai knowledge init creates:

   • knowledge/ directory with skeleton files (INDEX.md, patterns.md, gotchas.md, changelog.md)
   • skills/knowledge-scan-skill/SKILL.md — instructs agents how to perform deep analysis
   • /learn slash command for each enabled tool (Claude, Gemini, Antigravity, Copilot)

2. Your AI agent does the rest — using MCP tools (knowledge_explore, knowledge_append, knowledge_populate_ai_md) or by reading the skill directly. The agent understands semantics — it identifies patterns, gotchas, and architectural decisions that no static scanner can.

Why AI-driven? CLI scanners extract exports and file structure, but they miss context — why something is designed a certain way, what not to do, hidden dependencies. AI agents understand semantics and produce dramatically better knowledge.

Knowledge Commands

Command	Description
dotai knowledge init	Scaffold knowledge directory + /learn command + scan skill
dotai knowledge serve	MCP stdio server (runs independently, no init required)
dotai knowledge status	Show knowledge base health
dotai knowledge clean	Delete knowledge base for fresh start

MCP Integration

The MCP server runs independently — no dotai init required. It auto-creates the knowledge directory if missing. Add to .ai/settings/claude.json:

{
  "mcpServers": {
    "dotai-knowledge": {
      "command": "npx",
      "args": ["dotai", "knowledge", "serve", "--stdio"]
    }
  }
}

IDE tools (Antigravity): Add "--project", "/path/to/your/project" to the args array. IDE-spawned processes may not use your project as the working directory.

Agents then have access to 7 MCP tools:

Tool	Direction	Description
knowledge_query	📖 Read	Search the knowledge base by keyword
knowledge_get_module	📖 Read	Get full summary of a specific module
knowledge_list_modules	📖 Read	List all indexed modules
knowledge_recent_changes	📖 Read	Get recent codebase changes
knowledge_append	Write	Persist a finding (auto-creates missing files)
knowledge_explore	📖 Read	Read source files for deep AI analysis
knowledge_populate_ai_md	✏️ Write	Update AI.md project sections from codebase analysis

Auto-Persist: How Agents Write Back

The AI.md template includes a mandatory auto-persist rule. When an agent reads or modifies code and discovers something non-obvious (a gotcha, a hidden dependency, a pattern), it is instructed to immediately call knowledge_append without waiting for user prompts.

Persistence happens during the session as a side-effect of work — not at session close. This means knowledge accumulates across conversations automatically:

Session 1:  Agent discovers 10 things → persists 8 → knowledge base grows
Session 2:  Agent reads knowledge → starts smart → discovers more → persists again
Session 3:  Even richer context from line one

Agents can also be prompted explicitly:

/learn The PaymentService.processRefund() requires ROLE_ADMIN — calling without it throws 403 silently

Troubleshooting: nvm + IDE-based tools

If Node.js is installed via nvm, IDE-spawned tools (Antigravity) can't find npx because they don't load .bashrc. Use the full path + explicit env in your settings JSON:

{
  "mcpServers": {
    "dotai-knowledge": {
      "command": "/home/YOUR_USER/.nvm/versions/node/vXX.XX.X/bin/npx",
      "args": ["dotai", "knowledge", "serve", "--stdio", "--project", "/path/to/your/project"],
      "env": {
        "PATH": "/home/YOUR_USER/.nvm/versions/node/vXX.XX.X/bin:/usr/local/bin:/usr/bin:/bin"
      }
    }
  }
}

Find your path: which npx

Developer Workflow

One-time setup:

dotai init                        # 1. create .ai/ + symlinks
dotai knowledge init              # 2. scaffold knowledge + /learn command
# 3. Ask your agent: /learn

Daily workflow:

Code normally → Open AI agent → reads knowledge → starts smart
→ discovers more → auto-persists via knowledge_append

SDD Toolkit

dotai sdd brings Spec-Driven Development (SDD) to your project — a structured workflow where every piece of AI-generated code traces back to a human-reviewed specification.

The 8-Phase Workflow

Phase 1: Initiate     → Human writes idea.md
Phase 2: Specify      → Agent generates requirements.md       ← Human review
Phase 3: Decompose    → Agent breaks into tasks/*.task.md     ← Human review
Phase 4: Plan         → Agent generates plans + evaluation    ← Human review
Phase 5: Implement    → Agent implements following the plan
Phase 6: Evaluate     → Agent verifies against acceptance criteria
Phase 7: Review       → Agent produces holistic code review   ← Human review
Phase 8: Context-sync → Agent updates .ai/knowledge/

Quick Start

# 1. Initialize SDD toolkit
dotai sdd init

# 2. Create a new feature
dotai sdd new user-authentication

# 3. Write your idea
# Edit .ai/sdd/user-authentication/idea.md

# 4. Run phases using your AI tool's native commands:
#    Claude: /sdd-specify user-authentication
#    Gemini: /sdd-specify user-authentication
#    Copilot: Use prompt sdd-specify
#    Antigravity: Use workflow sdd-specify

SDD Commands

Command	Description
dotai sdd init	Scaffold skills, templates, and 28 cross-tool commands
dotai sdd init --force	Re-write skills and commands (preserves feature dirs)
dotai sdd new <name>	Create a new feature directory from template
dotai sdd list	List all features with their current phase
dotai sdd status [name]	Show phase-by-phase progress for a feature

Cross-Tool Phase Commands

SDD generates native commands for all 4 supported tools:

Phase	Claude / Gemini	Copilot	Antigravity
Specify	/sdd-specify	Prompt sdd-specify	Workflow sdd-specify
Decompose	/sdd-decompose	Prompt sdd-decompose	Workflow sdd-decompose
Plan	/sdd-plan	Prompt sdd-plan	Workflow sdd-plan
Implement	/sdd-implement	Prompt sdd-implement	Workflow sdd-implement
Evaluate	/sdd-evaluate	Prompt sdd-evaluate	Workflow sdd-evaluate
Review	/sdd-review	Prompt sdd-review	Workflow sdd-review
Sync	/sdd-sync	Prompt sdd-sync	Workflow sdd-sync

Running Phase Commands

The argument to every phase command is the feature name — not an individual file:

# Claude / Gemini CLI:
/sdd-implement user-authentication

# If you omit the name, the agent lists features and asks:
/sdd-implement

How each phase processes work:

Phase	Scope	Behavior
Specify	Entire feature	Reads idea.md, produces one requirements.md
Decompose	Entire feature	Reads requirements.md, produces all task files at once
Plan	Entire feature	Generates plans and evaluation criteria for all tasks in one shot
Implement	One task	Implements the lowest-indexed incomplete task, then stops and waits
Evaluate	One task	Evaluates the most recently implemented task — PASS → next, FAIL → retry
Review	Entire feature	Holistic review of the complete implementation
Sync	Entire feature	Updates knowledge base with all decisions and patterns

Implement and Evaluate are sequential by design. The agent works on one task at a time so you can inspect progress between tasks. Run /sdd-implement again to advance to the next task. If evaluation fails, the agent retries the same task automatically before moving on.

.ai/sdd/my-feature/
├── idea.md                        ← Phase 1: you write this
├── requirements.md                ← Phase 2: agent generates
├── tasks/
│   ├── 01_user_auth.task.md       ← Phase 3: agent generates
│   └── 02_api_routes.task.md
├── plans/
│   ├── 01_user_auth.plan.md       ← Phase 4: agent generates
│   └── 02_api_routes.plan.md
├── evaluation/
│   ├── 01_user_auth.evaluation.md ← Phase 4: acceptance criteria
│   ├── 01_user_auth.result.md     ← Phase 6: pass/fail verdict
│   └── ...
└── code-review.md                 ← Phase 7: holistic review

Resource Management

dotai v3.1.0 introduces CLI commands to manage all .ai/ resources without manually editing files.

MCP Servers

Add, remove, and list MCP server configurations across all enabled tool settings files.

# Add an MCP server to all tools
dotai mcp add my-server -c npx -a "@my-org/server,serve,--stdio"

# Add with environment variables
dotai mcp add db-server -c npx -a "db-mcp,--stdio" -e "DB_URL=postgres://localhost:5432/mydb"

# Add to only Claude
dotai mcp add claude-only-server -c npx -a "my-pkg" --tool claude

# List all configured servers
dotai mcp list

# Remove a server
dotai mcp remove my-server

Skills

Create and manage reusable skill packages in .ai/skills/.

dotai skill add code-review -d "Code review checklist"
dotai skill list
dotai skill remove code-review

Rules

Manage coding rule files in .ai/rules/ with YAML frontmatter.

dotai rule add api-conventions --always    # always apply
dotai rule add testing-guidelines          # on-demand
dotai rule list

Slash Commands

Create cross-tool slash commands. dotai cmd add creates format-appropriate files for every enabled tool:

Tool	Directory	Format
Claude Code	commands/	.md
Gemini CLI	commands-gemini/	.toml
Antigravity	workflows/	.md
Copilot	prompts/	.prompt.md

dotai cmd add deploy         # creates files for all enabled tools
dotai cmd list               # shows commands merged across formats
dotai cmd remove deploy      # removes from all formats

Built-in Slash Commands

dotai init automatically creates these slash commands for all enabled tools:

Command	Description
/review	Review code changes and provide feedback
/deploy	Guide through the deployment process
/learn	Deep codebase scan — populate .ai/knowledge/
/git-stage-commit	Stage all changes, generate commit message, commit locally (no push)

/git-stage-commit also checks whether the knowledge base has been populated — if .ai/knowledge/ exists but is empty, it runs the /learn flow first.

Config

View and modify .dotai.json settings directly.

dotai config show            # dump full config
dotai config get tools       # get a specific key
dotai config set aiDir .ai   # set a value (restricted keys)

Usage

Initialize a new project (interactive)

dotai init

Note: If you have existing CLAUDE.md, GEMINI.md, or .github/copilot-instructions.md files, dotai init automatically detects them and imports their content into .ai/AI.md — nothing is lost.

Initialize with defaults (selects all tools)

dotai init --yes

Restore from .dotai.json after cloning

# If .dotai.json exists, dotai init reads it and sets up everything automatically
dotai init

Initialize with specific tools

dotai init --tools claude,gemini,copilot

Check symlink health

dotai status

Fix broken symlinks

dotai doctor --fix

Add a new tool later

dotai add copilot

Force re-link (backs up and replaces existing files)

dotai link --force --backup

Remove a tool

dotai remove gemini

Upgrade scaffold files to latest version

dotai upgrade              # smart update — new files, stale cleanup, manual review
dotai upgrade --dry-run    # preview without changes
dotai upgrade --force      # overwrite ALL files (destructive)

upgrade creates new template files, auto-updates reference docs, removes obsolete files from previous versions, and saves user-modified files to _upgrade/ for manual review.

The .ai/AI.md File

This is the heart of dotai. Write your project context once:

# AI Instructions — MyProject

## Architecture
- src/api/       — REST API routes (Express.js)
- src/services/  — Business logic layer
- src/models/    — Database models (Prisma)

## Tech Stack
- TypeScript 5.x, Node.js 20, PostgreSQL 16

## Key Commands
| Action | Command |
|--------|---------|
| Dev    | `npm run dev` |
| Test   | `npm test`    |
| Build  | `npm run build` |

## Important Constraints
- NEVER use `any` type
- ALWAYS run tests before committing

Every AI tool sees this content through its own native config path.

Platform Support

Platform	Symlink Type	Notes
macOS / Linux	Standard symlinks	Works out of the box
Windows 10+	NTFS junctions (dirs) + symlinks (files)	No admin privileges needed

All symlinks use relative paths for portability — move or clone the repo anywhere and dotai link recreates everything.

After Cloning

When a teammate clones the repo, they just run:

npm install -g @nbslabs/dotai  # if not already installed
dotai init            # reads .dotai.json, scaffolds missing files, links everything

dotai init detects the existing .dotai.json and automatically sets up the project — no prompts, no tool selection. Just like npm install reads package.json.

Git Integration

• ✅ Commit the .ai/ directory — it is your source of truth
• ✅ Commit .dotai.json — it tracks which tools are configured
• ❌ Don't commit .claude/, .gemini/, etc. — dotai adds them to .gitignore automatically

Development

git clone https://github.com/nbslabs/dotai-cli.git
cd dotai-cli
npm install
npm run dev     # Watch mode (rebuilds on save)
npm test        # Run test suite (Vitest)
npm run build   # Production build
npm run lint    # TypeScript type check

Contributing

Contributions are welcome! Please open an issue first to discuss what you'd like to change.

1. Fork the repo
2. Create a feature branch (git checkout -b feature/amazing-thing)
3. Commit your changes (git commit -m 'Add amazing thing')
4. Push to the branch (git push origin feature/amazing-thing)
5. Open a Pull Request

License

MIT