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This quick start guide will help you build your first AI-ready local knowledge base with Linkly AI in just a few minutes, and learn the basic usage.
Want the easy way? Let an AI install it for you. If you already have an AI assistant that can run commands — Claude Code, Codex, Cursor, and the like — send it the line below. It will read the Setup Guide for Agents and walk you through installation, configuration, and verification step by step — including the parts you have to do yourself, which it will spell out clearly.
Of course, reading on is perfectly fine too — this page is a complete manual setup guide in its own right.

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Before You Begin

Linkly AI includes the following core applications and capabilities:

Linkly AI Desktop

The desktop application (referred to as Linkly AI). After installation, it automatically indexes documents and provides search, outline, and reading tools.

Linkly AI CLI

A command-line tool that connects to your Linkly AI app via Bash and invokes its tools. Ideal for AI Agent usage.

MCP Server

An open protocol for Agents to retrieve context. The MCP service starts automatically after installing Linkly AI. Ideal for AI Agent invocation.

linkly-ai-skills

Official Agent Skills that guide Agents on how to connect and use Linkly AI’s tool services. Strongly recommended.

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Step 1: Install Linkly AI

Go to the official download page and select the version for your operating system:

Download Linkly AI

Choose the version for your operating system
Then double-click the installer. Installation steps for each platform:
1

Open the installer

Double-click the downloaded .dmg file to mount the disk image
2

Drag to Applications

Drag the LinklyAI icon into the Applications folder
3

Launch the app

Find LinklyAI in Launchpad or the Applications folder in Finder, and double-click to launch

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Step 2: Initialize Linkly AI

When you first launch Linkly AI, a guided window walks you through the setup. After that, you add your own documents:
1

Complete the first-launch wizard

The wizard has four screens — cover → Bring your files in → Connect an agent → All set (the “1 / 2” and “2 / 2” in the bottom-right corner only count the middle two). Two small buttons in the bottom-right corner of each screen’s top panel let you switch the language and appearance at any time.
  • Cover: tick I have read and agree to the Privacy Policy — this is required to continue. The Help improve Linkly AI (anonymous) telemetry toggle below it is on by default and can be turned off.
  • Bring your files in: Sample files is required; it is unpacked and indexed in the background as soon as the wizard opens. Below it are your system’s Documents, Desktop, and Downloads folders, unticked by default — tick one and it starts indexing. The first time macOS reads these folders it shows a system permission prompt; if you decline, the row shows Not authorized.
  • Connect an agent: click Install to have the Linkly CLI and Skills installed in the background; if you don’t click it, nothing is installed. Keep the CLI and Skills up to date is on by default. This screen also has a setup instruction you can send straight to your agent.
  • All set: click Get started to finish the wizard and land on the main window’s home page. The checklist at the top of the home page then walks you through adding folders, connecting an agent, and more.
The wizard has no sign-in step. Local indexing, local search, and the MCP service all work without signing in. To use the official AI models, sign in under Settings → Account; if you are not signed in and have no other model configured, the Ask page will prompt you to sign in.
2

Add your own documents

If you didn’t tick any folders during the wizard, only the sample files are indexed. Your own files are not indexed yet. Skip this step and searches will never turn up your real content.
Either approach works:
  • Open Library in the main window’s sidebar, click Add folder in the left column, and pick the directories you want indexed — Documents, Downloads, a project directory, and so on;
  • Or drop files into the ~/LinklyAI folder. It is watched by default, so anything you put there is indexed automatically.
If the system reports insufficient permissions (common on macOS), go to System Settings → Privacy & Security → Full Disk Access, add Linkly AI, then restart the app.
3

Connect your AI tools

Add Linkly AI’s MCP service to your frequently used AI tools for intelligent document search.
We recommend using Skills to assist with integration — it’s the simplest approach. Just copy the following prompt to your AI assistant and follow the instructions to complete both tool and Skills integration:

Please install Agent Skill linkly-ai-skills and...

You can also manually integrate the MCP tools, but we still recommend installing Skills for a better experience:
Run in your terminal:
60606 is the default port for Linkly AI’s MCP service. If you can’t connect, check the actual port in the MCP Server: Running (port …) line of the tray menu, or click View MCP connection settings on the Agent usage page of the main window.

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Step 3: First Use

After launch, Linkly AI will immediately start indexing your documents and continuously monitor for changes. Full indexing will complete within a few minutes to tens of minutes (depending on the number of documents and machine performance).
After the first launch, Linkly AI downloads about 890MB of model files in the background — roughly 639MB for semantic search and 249MB for OCR. Depending on your connection this can take from a few minutes to over an hour.Keyword search works right away and is unaffected. Natural language (semantic) search becomes available once the download and indexing have both finished.
Got meeting recordings, podcasts, or course videos to search? Speech transcription for audio and video is off by default — those files still get indexed and can be found by filename, but you can’t search what was said inside them. Open the Index management page (click the index icon at the bottom of the main window’s left sidebar, or right-click the tray icon and choose View Index) and turn on Audio transcription and Video transcription under Extraction enhancements — the app works through your existing files automatically. Every index switch is documented in Index Settings.
You have two ways to use Linkly AI:

Search documents with the Launcher

Use the global shortcut ⌘ + L (Ctrl + L on Windows / Linux) to open the search launcher window, then enter keywords or descriptive language to find target documents. You can also right-click the L icon in the system tray and choose Search from the menu (left-clicking the tray icon opens the main window instead). Users upgrading from an older version keep their existing shortcut, which you can check under Settings → Shortcuts.You can further preview, view metadata, open documents, copy links, and more. For detailed usage, see the Full-Text Search Launcher documentation.

Use with AI Agents

This is our more recommended approach — you’ll enjoy an unprecedented interactive experience and research efficiency.After integrating with your AI assistant or installing Skills, append use linkly-ai after any prompt to actively leverage Linkly AI’s powerful search capabilities.