MCP Integrations

MCP (Model Context Protocol) lets you extend Qualia with external tools. Connect services like GitHub or Linear—and Qualia can use them during your conversations. Some connectors, such as Slack, are built into Qualia instead and need no MCP server at all.

What is MCP?

MCP is a standard protocol for connecting AI assistants to external capabilities:

Servers provide tools (functions the AI can call)
Qualia connects to servers and exposes their tools
You control which servers are enabled and what permissions they have

When you add an MCP server, Qualia can then use those tools to accomplish tasks.

In Qualia Cloud you can add any MCP server that has a URL, authenticating it with a header if the server needs one. Your servers are yours alone: another person on the same deployment cannot see them, and the headers you configure are encrypted.Linear, Atlassian, Sentry, Notion, and Stripe support browser sign-in in cloud and desktop. Google Drive and BigQuery use built-in tools with Google sign-in directly in the connector browser in both builds. GitHub uses its official remote server and your GitHub credential saved in Settings. Command-based (stdio) servers remain Desktop only in the catalog. Databricks, Snowflake, Postgres, and Slack work in both cloud and desktop.

Signing in to a cloud connector

Open Customize agent > MCP Servers > Browse connectors, choose Linear, Atlassian, Sentry, Notion, or Stripe, and install it. Select Sign in on the server to authorize access in the same browser tab. Complete sign-in in the browser where you started it; opening the authorization link in another browser will fail. After authorization, choose Return to Qualia to load the connector’s tools and return to the workspace where you started sign-in. If loading tools fails, return to the workspace and choose Refresh tools. To revoke a connector’s authorization, select it and choose Unlink account. Deleting the server alone keeps authorization for reinstalling it. Changing its URL or OAuth client may require signing in again. Desktop GitHub uses a fine-grained personal access token; the GitHub App is offered when the deployment supports it. The GitHub catalog connector uses that App or token saved in Settings > Integrations > GitHub. The credential is sent only to GitHub’s official MCP endpoint.

Adding an MCP server

Google Drive and BigQuery

Open Customize agent > MCP Servers > Browse connectors, then choose Google Drive or BigQuery. For BigQuery, enter the Execution and billing project first. Click Connect with Google, approve access, and select Return to Qualia. Each service connects independently; connecting the second service asks for its additional permission. BigQuery can discover datasets, tables, and schemas in your saved project and run read-only SELECT queries. Your Google account needs permission to run jobs in that project and read the queried tables. Google bills the saved project. Each query is limited to 1 GB billed, 1,000 result rows, and two minutes. Google Drive can search and read files you can access, including shared drives. Docs are read as text, Sheets as CSV of the first sheet, and Slides as text. Files must be no larger than 10 MiB. Files with download restrictions remain restricted. Select Google Drive or BigQuery in the MCP Servers list, or reopen it in Browse connectors, to see your Google account, reconnect, or disconnect. To change BigQuery’s billing project, edit it and choose Reconnect with Google. Disconnecting one service keeps the other connected; disconnect both before switching Google accounts. If connections are unavailable, contact your Qualia administrator. On desktop, connect Qualia Cloud in Settings first. Connect with Google opens your default browser. If asked, sign in to the same Qualia account you use on desktop, then authorize Google and return to the desktop window. The connection status updates automatically. Cloud and desktop share your Google authorization and billing project. Disconnecting in either build affects both. Drive downloads are saved in the workspace where you use the connector.

OneDrive: file access without Copilot

In Customize agent > MCP Servers > Browse connectors, choose OneDrive, then Connect with Microsoft. This connector uses Microsoft Graph with read-only file access; it does not require a Copilot license. Desktop opens your browser for sign-in and uses your Qualia Cloud account connection. If Microsoft connections are unavailable, contact your Qualia administrator to enable them. Qualia can search your OneDrive, list folders, and read Word (.docx) or UTF-8 text files up to 50 MiB. Word extraction includes main-document paragraphs and tables, but not headers, footers, comments, or images. File IDs come from search or folder results. This connector currently targets your own OneDrive; it does not offer SharePoint-library browsing or resolve arbitrary sharing links. Some complex Word files may be too large to read even below the file-size limit. If that happens, split the document or export it as text. Ask Qualia to read the document again when you need the latest OneDrive version. Ask Qualia to find a document, summarize its contents, compare documents, or use them as source material for your analysis. Reconnect if Microsoft revokes access. Disconnecting OneDrive removes Qualia’s saved tokens; it does not revoke the app’s consent in Microsoft.

Custom servers

Open a workspace in Qualia.
Open the gear menu in the titlebar, click Customize agent, and choose MCP Servers.
Click New custom server, or Browse connectors for a preconfigured one.
Configure the server using the fields below, then click Create. If the server needs OAuth, click Sign in and complete the browser flow.

Command-based (stdio)

For servers that run as local processes:

Name: Identifier for this server
Command: The executable to run (e.g., npx, python)
Arguments: Command-line arguments
Environment variables: Variables to set for the process

Add any tokens or settings the server needs under Environment variables; do not rely on variables exported in your shell. Command-based servers are available on single-user desktop connections. Use a URL-based server for Qualia Cloud or a shared deployment.

URL-based (HTTP/SSE)

For servers accessible via HTTP:

Name: Identifier for this server
URL: The server endpoint
Headers: Authentication headers (optional)

On desktop, use an http or https URL, including a local server such as http://localhost:3000/mcp. Qualia Cloud requires a publicly reachable destination; OAuth sign-in also requires HTTPS. On a local desktop connection, headers can reference saved credentials with ${quadrillion:credential:LINEAR_API_KEY}. For custom servers on shared deployments, enter the authentication header directly. The catalog GitHub connector uses your GitHub credential saved in Settings.

Pasting configuration

You can paste JSON configuration directly:

{
  "my-server": {
    "command": "npx",
    "args": ["-y", "my-mcp-server"]
  }
}

This format is compatible with Cursor’s mcp.json, making it easy to share configurations.

Managed connectors

Some connectors are managed by a native Qualia integration rather than configured by hand. They appear in the connector catalog, but signing in happens once in settings and the credentials are handled for you — there is no token to paste and nothing written to mcp.json. GitHub is the exception: you connect the Qualia GitHub App or paste a fine-grained token once in Settings, and the connector reads that credential from there. A managed connector can also show up in the MCP Servers list itself — a connected Databricks Genie Space appears there as databricks-genie. Such entries are read-only: they cannot be edited, renamed, disabled, or deleted from the list, only from the owning integration’s settings page. Select Slack or databricks-genie to see a Managed connection notice above its tools. Click Manage connection to open Settings → Integrations, then find the Slack or Databricks group. You can still refresh tools and change their permissions in the MCP Servers panel. Google Drive, BigQuery, and OneDrive keep their connection controls directly in this panel.

Connector	Set up in
Databricks (Genie)	Settings → Integrations → Databricks
Slack	Settings → Integrations → Slack
Snowflake	Settings → Integrations → Snowflake; desktop signs in on the first query, after saving settings
Postgres	Settings → Integrations → Postgres
GitHub	Settings → Integrations → GitHub

Connecting GitHub does one thing beyond the connector itself: it lets Qualia reach your private repositories. Clone one into an empty workspace — File actions → Clone from GitHub, or the button on the empty workspace itself — and Qualia authenticates as you (see Cloning a repository). You can also just ask the agent to clone a repository. Public repositories work without connecting anything. There are two ways to grant that access. Both are managed from Settings → Integrations → GitHub, and the clone dialog offers them right where you need them.

Connect the Qualia GitHub App (Qualia Cloud). One click opens GitHub, where you pick the account and the repositories Qualia may read. The App can only read repository contents, metadata, issues, and pull requests — you cannot grant it more by accident — and its access token expires every eight hours, renewed automatically while you keep using Qualia. Install it on your own account and on your organization and both sets of repositories work. Add or remove repositories later with Manage on GitHub. If a clone is refused because the App does not cover that repository, the dialog links straight to the page that fixes it — installing the App on that account, or adding the repository to the list it already has there.
Paste a fine-grained personal access token. The fallback for the desktop app, for organizations that block third-party GitHub Apps, and for anyone who prefers a token. Only fine-grained tokens (they start with github_pat_) are accepted: classic tokens and OAuth sign-in grants carry the repo scope, which is read and write access to every repository you can reach, and GitHub does not let you narrow it. A token is bound to one account or organization, so use the App if your repositories span several.

When both are set up, the App is used for every repository, including ones it is not installed on; the token is used only while the App is disconnected or its connection has expired. If a repository is reachable by your token but not by the App, add it to the App’s installation on GitHub, or disconnect the App to clone with the token.

What the token needs

One credential serves both cloning and the GitHub connector, so scope it for whichever you use. Restrict it to the specific repositories you want reachable.

Permission	Needed for
Contents: Read-only	Cloning a private repository
Metadata: Read-only	Granted automatically alongside Contents
Contents: Read and write	Only if you want the agent to push
Issues / Pull requests: Read-only	Connector tools that read issues or PRs

If you only clone, Contents and Metadata read-only are enough. On desktop, neither is needed for cloning: Qualia uses the git credentials already configured on your machine, the same ones git clone uses in your terminal. The token still matters there for the GitHub connector. Cloning defaults to Latest commit only, which is much faster and much smaller. Turn it off when you need history, or when a build reads git log or derives its version from tags.

Save your token in Settings rather than putting it in a repository URL, which can expose it in your workspace files.

Databricks is worth calling out. In Qualia Cloud it is organization-scoped, so an admin configures the workspace once and each member then signs in individually; on desktop you configure and sign in yourself. Genie answers arrive labeled Powered by Genie with a link to the Space that produced them. Connect and authorize each integration before asking the agent to use it. For Databricks Genie, also select a Genie Space. If you connect a service during an agent turn, send another message afterward to use its tools; on desktop, allow up to a minute for the connection to appear.

Server status

Each server shows its connection status:

Status	Meaning
Connected	Server is running and tools are available
Connecting	Attempting to establish connection
Disconnected	Not currently connected
Error	Connection failed (click for details)
Disabled	Server is configured but turned off

Use the Enable/Disable toggle to control whether a server should connect.

Managing tools

Click a server to expand its tool list. Each tool shows:

Name: What the tool is called
Description: What the tool does
Permission: How confirmations are handled

Tool permissions

Control how each tool runs:

Permission	Behavior
Always	Run without asking
Require permission	Ask before each use
Never	Block this tool entirely

New tools default to Require permission. When Qualia wants to use a tool with this setting, an approval request appears above the message box showing what it wants to do. Choose Run to approve this use, or Skip to decline — Qualia is told you declined and continues without the tool. You can pick Always allow from the request’s dropdown to approve future uses.

Viewing schemas

Click Show schema on any tool to see its input schema — the parameters it accepts and their types. This helps you understand what the tool can do.

Tool usage in chat

When Qualia uses an MCP tool:

A tool call row appears in the agent activity stream, labeled with the connector’s logo and a friendly name (e.g. “Ran Slack: read channel”). Expanding it shows the arguments as a collapsible tree
For “Require permission” tools, an approval request appears above the message box with the same logo, tool name, and arguments
After approval (or for “Always” tools), the tool executes
Results appear in the row: JSON results render as a collapsible tree with copy buttons, text renders as-is, and resource links are clickable. The maximize button opens the full result in a dialog

Only connect MCP servers you trust. Servers may access your data and chats.

Refreshing tools

If a server’s tools change, click Refresh tools to rediscover them. This is useful during server development or after updates.

Configuration file

MCP configuration is stored as mcp.json in your Qualia config directory — macOS ~/Library/Application Support/io.quadrillion.qualia, Windows %APPDATA%\io.quadrillion.qualia, Linux $XDG_CONFIG_HOME/io.quadrillion.qualia, defaulting to ~/.config/io.quadrillion.qualia — alongside settings.json:

{
  "mcpServers": {
    "my-server": {
      "command": "npx",
      "args": ["-y", "my-mcp-server"],
      "enabled": true,
      "tool_permissions": {
        "some-tool": "always"
      }
    }
  }
}

You can edit this file directly — changes are picked up automatically. Use Customize agent > MCP Servers > Browse connectors to find preconfigured servers.

Timeouts

Two optional per-server fields bound how long Qualia waits on a server. Both are in seconds, and you only need to set them if a server legitimately needs longer than the default.

Field	Default	Covers
`startup_timeout_seconds`	30	Connecting to the server and listing its tools
`tool_call_timeout_seconds`	30	A single tool call

{
  "mcpServers": {
    "slow-server": {
      "url": "https://example.com/mcp",
      "startup_timeout_seconds": 30,
      "tool_call_timeout_seconds": 120
    }
  }
}

Raise startup_timeout_seconds for a server that is genuinely slow to boot. A stdio server started with npx -y is slowest on its very first run, when the package still has to be downloaded. Raise tool_call_timeout_seconds for tools that do long-running work.

Troubleshooting

Server won’t connect

Check the command/URL is correct
Verify required dependencies are installed
Look at the error message for specifics

Server stops responding

If a server accepts the connection but never answers, Qualia gives up after startup_timeout_seconds, marks it Error, and tells you in chat rather than leaving the request hanging. This usually means a wrong command or URL, a missing dependency or credential, or a command that is waiting for input it will never receive. If the server is simply slow to start, raise startup_timeout_seconds.

Server needs signing in again

A server that authenticates with OAuth issues Qualia a token that eventually expires. When it cannot be renewed on its own, the server says it needs an OAuth login and offers a Sign in button; its tools stop working until you click it and complete the flow in your browser. Complete authorization and any multi-factor authentication in your browser, then return to Qualia.

Server needs an OAuth client

Most servers that sign in through OAuth let Qualia register itself with their sign-in provider the first time you connect, so there is nothing to configure. A few do not — custom GitHub OAuth setups, Slack’s remote server, and Microsoft Entra, which expects each customer to register the app in their own tenant. Those fail before a browser ever opens, with a message saying the server needs an OAuth client. To connect one, register an OAuth app with that provider yourself, then open the server in Customize agent > MCP Servers, click Edit, expand OAuth client and fill in:

Client ID — from the app you registered. Required.
Client secret — only if the provider issued one. Leave it empty for a public client, which authenticates with PKCE instead.
Redirect URI (desktop) — must be one the app is registered with, and must be a loopback address with a port, such as http://localhost:8400/callback. Leave it empty when the provider accepts any loopback port, and Qualia picks a free one.

In Qualia Cloud, leave Redirect URI empty and register the deployment’s fixed API callback, https://<deployment-api-host>/api/mcp/oauth/callback, with the provider. Replace <deployment-api-host> with your deployment’s API hostname. The catalog’s five OAuth connectors register this automatically. GitHub from the catalog reuses Settings credentials and needs no custom OAuth client. Sign in again after changing the client ID. For GitHub, generate a client secret in your OAuth app’s settings and enter it along with the client ID. Register the same loopback redirect URI you enter in Qualia, then click Sign in on the server. Slack has a further requirement that a client ID alone does not satisfy: the app must be published to the Slack directory or be internal to your workspace, and a workspace admin has to approve MCP servers.

Tools not appearing

Click Refresh tools
Check server status is “Connected”
Verify the server actually provides tools

Permission issues

Tools default to “Require permission”
Change to “Always” for trusted, frequently-used tools
Use “Never” for tools you want to block

Welcome

Core Features

Research Workflow

Tools

Customization & Settings

Interface

What is MCP?

Signing in to a cloud connector

Adding an MCP server

Google Drive and BigQuery

OneDrive: file access without Copilot

Custom servers

Command-based (stdio)

URL-based (HTTP/SSE)

Pasting configuration

Managed connectors

What the token needs

Server status

Managing tools

Tool permissions

Viewing schemas

Tool usage in chat

Refreshing tools

Configuration file

Timeouts

Troubleshooting

Server won’t connect

Server stops responding

Server needs signing in again

Server needs an OAuth client

Tools not appearing

Permission issues

​What is MCP?

​Signing in to a cloud connector

​Adding an MCP server

​Google Drive and BigQuery

​OneDrive: file access without Copilot

​Custom servers

​Command-based (stdio)

​URL-based (HTTP/SSE)

​Pasting configuration

​Managed connectors

​What the token needs

​Server status

​Managing tools

​Tool permissions

​Viewing schemas

​Tool usage in chat

​Refreshing tools

​Configuration file

​Timeouts

​Troubleshooting

​Server won’t connect

​Server stops responding

​Server needs signing in again

​Server needs an OAuth client

​Tools not appearing

​Permission issues

What is MCP?

Signing in to a cloud connector

Adding an MCP server

Google Drive and BigQuery

OneDrive: file access without Copilot

Custom servers

Command-based (stdio)

URL-based (HTTP/SSE)

Pasting configuration

Managed connectors

What the token needs

Server status

Managing tools

Tool permissions

Viewing schemas

Tool usage in chat

Refreshing tools

Configuration file

Timeouts

Troubleshooting

Server won’t connect

Server stops responding

Server needs signing in again

Server needs an OAuth client

Tools not appearing

Permission issues