MEASURED 14.5× faster · 13.3× leaner on the same task, same agent, same repo See the method
DEVELOPER ONBOARDING GUIDE

Getting Started with Helixor Code.

Helixor Code gives Claude Code, Codex, Cursor, Antigravity, Gemini, and Grok a persistent, living structural code graph and stateful TODO memory over the Model Context Protocol (MCP) — running locally with zero cloud keys required to start.

FULL DOCUMENTATION Looking for the complete technical reference?

Deep dive into our 6-part technical documentation: CLI Reference, Code Indexing, Local Desk Web UI, Menu Bar Tray, and Agent Rules.

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01 Create an Organization & Log In

Go to code.helixor.dev to create an organization and log in. Once registered, you can manage your team and access shared workspaces. You will connect this account to your local development environment during helixor init after installing the CLI.

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02 Operational Modes

Helixor Code operates across two flexible tiers designed to meet teams wherever they are in their AI adoption journey:

Augment Mode · Free · No Key

Drop into your existing agent

Attaches to Claude Code, Codex, Cursor, Antigravity, Gemini, or Grok via local MCP. The agent brings its model; Helixor provides structural code search (code.search, code.impact.analyze) and stateful TODO stacks (brain.todo). Saves 6×+ token overhead by substituting AST motifs for whole-repo file dumps.

Orchestrate Mode · Enterprise · BYOK

Governed multi-LLM operational pipelines

Runs checkpointed, resumable operational pipelines where specialized models handle specific steps (Claude or Gemini verifies plans, human approves at the gate, Codex or Grok implements and audits) on your own keys with audit trails and shared team memory.

See detailed architecture in How It Works or review the Documentation Overview.

03 Prerequisites & Installation

Helixor Code runs on macOS (companion daemon + menu-bar tray app) and Linux (headless systemd service + HTTP status API). Requires Python 3.11+.

Standard Installation via PyPI (Recommended with pipx):

# Install pipx if needed (macOS: brew install pipx && pipx ensurepath) pipx install helixor # Or standard user install via pip: pip install --user helixor

Air-Gapped / Offline Installation:

# Using the pre-built offline bundle: cd helixor-wheelhouse ./install.sh

The installer automatically provisions an isolated environment at ~/.helixor-cli and links the binary onto your PATH. For full installation options and requirements, see the CLI Reference Docs.

04 First-Time Setup (helixor init)

Run the guided, interactive setup command to configure your local companion, background daemon, and project roots in one step:

helixor init

What helixor init configures:

  • Identity & Login: Sets up local credentials or runs offline with --skip-login.
  • Source Roots: Registers your repositories (e.g. ~/code).
  • Local Companion: Starts the unified local MCP listener.
  • Autostart Service: Configures a persistent user service (LaunchAgent on macOS, systemd on Linux).
  • Menu-Bar Tray: Launches the companion app with real-time token savings and health metrics.
  • Agent Detection: Detects installed coding agents (Claude Code, Codex, Antigravity, Gemini, Grok) and configures MCP automatically.

Common Setup Flags:

# Specify repository source root directly helixor init --source-root ~/code # Skip portal login for fully offline / local evaluation helixor init --skip-login # Build indexes immediately upfront helixor init --source-root ~/code --index-strategy eager # Connect directly to a team workspace hub helixor init --hub https://code.helixor.dev --organization-id org_12345

Detailed flags and environment variables are documented in CLI Lifecycle Documentation.

05 System Health & Diagnostics

Verify that your companion daemon and agent MCP registrations are fully operational:

helixor doctor

helixor doctor validates CLI release train, background daemon status, source roots, MCP tool responsiveness, and cloud portal sessions. For quick runtime endpoint status:

helixor status helixor status --json

Read more in Health & Diagnostic Commands.

06 Connecting Your AI Coding Agents

Helixor Code integrates with any MCP-compliant agent, IDE, or CLI. Each agent receives specialized rule files and instruction sets:

Claude Desktop & Claude Code

helixor agent install claude # Or compatibility shortcut: helixor claude install

Codex

helixor agent install codex # Writes registration to ~/.codex/config.toml

Cursor IDE

# Print pasteable MCP configuration snippet: helixor mcp-config

Google Antigravity, Gemini, Grok & Generic MCP Clients

helixor agent install antigravity # Configures Antigravity MCP registration & rules helixor agent install gemini # Configures Gemini CLI / extension helixor agent install grok # Writes ~/.grok/config.toml helixor agent install mcp-generic # Outputs standard MCP JSON for any other tool

See instructions for each agent runtime in Agent Rules & MCP Integration Guide.

07 IDE Plugins (VS Code, Cursor, JetBrains)

Bring living structural indexes, code quality findings, and TODO stacks directly into your editor sidebar:

  • VS Code / Cursor: Search for "Helixor Code" in the Marketplace or install from .vsix.
  • JetBrains (IntelliJ, PyCharm, WebStorm): Search "Helixor Code" under Settings → Plugins or install from .zip.
  • Adopt Workspace: Run Cmd/Ctrl+Shift+PHelixor: Adopt Current Workspace.
  • Push TODO from Selection: Highlight code and trigger Helixor: Push TODO Stack from Selection to anchor tasks directly to code symbols.

08 Repository Indexing & File Watching

Helixor uses lazy on-demand indexing by default, but you can build or rebuild indexes explicitly:

# Index a single repository helixor index /path/to/your/repo # Index with eager build for all submodules helixor index ~/code/project --index-strategy eager # Combine a multi-repo workspace root into a single unified index helixor index ~/code/monorepo --single-index # Reset index quarantine and rebuild cleanly helixor index-reset --yes

helixor up automatically starts a background debounced filesystem watcher. Modifying files refreshes indexes incrementally.

Learn how AST indices, freshness hashes, and project roots work in Code Indexing Documentation.

09 Day-to-Day Companion & Menu-Bar Tray

Control the companion daemon lifecycle with simple commands:

helixor up # Starts companion listener and macOS tray app helixor down # Stops companion and tray processes helixor status # Shows runtime health, listener PIDs, and active profiles

macOS Menu-Bar App Features:

  • Health Indicator: Real-time status (Healthy, Busy, Offline).
  • Token Savings Meter: Live counter of tokens consumed vs. tokens saved (averaging 6×+ reduction vs. raw grep).
  • Active TODO Stacks: Live view of in-flight TODO frames and design state.
  • Workflow Gate Watch: Monitor and approve pending operational pipeline approval gates.
macOS Menu Bar Tray COMPANION UP
Helixor Code macOS Tray Status
Local Desk at 127.0.0.1:18733/desk TODOs & STACKS
Helixor Code Local Desk Operations Surface

Explore the browser desk interface at Local Desk Guide and appliance status at Menu Bar Tray Guide.

10 MCP Tool Reference

Once connected, your agent has access to canonical Helixor MCP tools:

Code Intelligence Tools

ToolCapabilityExample Agent Prompt
code.search Structural AST search (definitions, usages, bonds, motifs). "Where is the JWT token verified in the auth middleware?"
code.impact.analyze Impact analysis across APIs, models, tests, and call graphs. "What components will break if I modify UserSession.role?"
code.tests.find Reverse query: finds tests covering specific behaviors. "Find test cases covering payment webhook retries."
code.review Architectural quality and motif assessment. "Review the auth package for anti-patterns and circular bonds."
code.diff Structural concept and working-tree diffs. "Show structural changes between main and this branch."

Durable Planning & Team Memory Tools

ToolCapabilityExample Agent Prompt
brain.todo LIFO subject-scoped stack of TODO frames (push, peek, update, pop). "Create a TODO stack for refactoring payments and mark step 1 done."
brain.design Durable design documents with phase lifecycle tracking. "Save our architectural design decisions for the database migration."
workspace.get Reads shared context, pinned decisions, and channel updates. "What decisions did the team pin in the release channel today?"
workspace.act Posts updates and pins decisions for cross-agent team handoff. "Post a summary of the auth refactor to the workspace channel."

Complete schema definitions and parameter guides are listed in the MCP Tools Reference.

11 Team Hub & Multi-Developer Synchronization

Collaborate across engineering teams on shared codebases with a spoke-and-hub architecture:

# Authenticate with your enterprise team hub: helixor login https://code.helixor.dev
  • Local Security: Source code and AST indexes remain local on each developer's machine (spoke).
  • Shared Memory: TODO stacks, designs, and workspace channels synchronize securely through the Hub.
  • Zero Network Friction: No VPN or inbound port forwarding required.

Read about enterprise network architecture in Hub-and-Spoke Overview.

12 Maintenance & Troubleshooting

One-Command Recovery (helixor repair):

If an agent integration goes stale, background processes conflict, or registrations mismatch, run:

helixor repair

helixor repair cleans up orphaned listeners, restarts the companion daemon, and re-validates MCP configurations across all installed agents.

Upgrading the CLI:

helixor update

Clean Uninstallation:

# Dry-run inspection: helixor uninstall # Clean removal of local companion, indexes, and registrations: helixor uninstall --yes # Also remove stored credentials: helixor uninstall --yes --forget-login

See troubleshooting recipes in Reconciliation and Recovery Docs.

13 Quick Command Summary

# Setup & Health helixor init # Guided one-command setup helixor login https://code.helixor.dev # Authenticate with organization hub helixor doctor # System diagnostics & MCP verification helixor status # View running companion & endpoints # Companion Lifecycle helixor up # Start companion & tray app helixor down # Stop companion & tray app helixor repair # Reconcile & fix broken agent/companion state helixor update # Upgrade CLI and reconcile dependencies # Agent Integrations helixor agent install claude # Register with Claude Desktop / Claude Code helixor agent install codex # Register with Codex (~/.codex/config.toml) helixor agent install antigravity # Register with Google Antigravity helixor agent install gemini # Register with Gemini helixor agent install grok # Register with Grok helixor mcp-config # Print JSON snippet for Cursor / other clients # Code Indexing helixor index /path/to/repo # Build structural AST code index helixor index-reset --yes # Clean rebuild of all local indexes
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Rule of thumb

Match the tool to the task.

One-off question

Just query code.search. Structural lookup answers with exact AST bonds — no whole-repo token waste.

Nontrivial change

Plan with brain.design and push a brain.todo stack so engineering intent survives across context limits.

Governed SDLC

Run multi-LLM workflows with human approval gates, evidence certificates, and checkpointed rollbacks.

Enterprise Sales & Onboarding

Deploy Helixor Code in your organization.

Augment mode is free for individual developers. Talk to our solutions team to configure enterprise hub synchronization and governed multi-LLM SDLC pipelines.