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Connect Atlassian to Cline CLI

Give Cline CLI governed access to Atlassian’s 96 tools through Runlayer, with identity, policy, scanning, and audit on every call.

Book a demo Cline CLI setup guide

Set up

Add Atlassian to Cline CLI in four steps

Admins approve the server once. Everyone in Cline CLI then gets it through the same governed connection.

  1. 1

    Approve Atlassian in Runlayer

    Add Atlassian from the catalog and choose who can use it and which of its tools are allowed.

  2. 2

    Connect Cline CLI to Runlayer

    Users add the Runlayer Plugin to Cline CLI by following Runlayer’s setup guide. Cline CLI reaches Atlassian’s 96 tools through the Runlayer Plugin’s search and execute tools instead of listing each one.

    Cline CLI setup guide
  3. 3

    Sign in to Atlassian

    Sign in the way Atlassian requires. Runlayer holds the credentials so they stay out of the client’s configuration.

  4. 4

    Use Atlassian from Cline CLI

    Atlassian’s approved tools appear in Cline CLI. Every call is checked against policy and recorded.

Tools

96 Atlassian tools in Cline CLI

Runlayer policy decides which of these Cline CLI users can call. 12 read data only and 1 can change or delete data.

  • Add comment to Jira issue

    Add or update a comment on a Jira issue

  • Add Confluence content permissions

    Adds one or more content-level permission grants to a single Confluence content entity.

  • Add Confluence reaction

    Add emoji reaction to Confluence content

  • Add connections to goals

    Add one type of connection to one or more Atlassian Goals.

  • Add connections to projects

    Add one type of connection to one or more Atlassian Projects.

  • Add Teamwork Graph context

    Adds a relationship between two entities in the Teamwork Graph (e.g. linking two Jira work items, marking one as blocking another, attaching a remote link, or connecting a Jira work item to an Atlas…

  • Add labels to Confluence content

    Add labels to any Confluence content (page, blogpost, attachment, custom content)

  • Add or edit Jira issue comment

    Add a comment to a Jira issue, or edit an existing one: omit commentId to add, or pass one from listJiraIssueComments to edit.

See all 96 Atlassian tools

Control

What Runlayer can see and stop in Cline CLI

Some controls apply to every client at the gateway. Others depend on what Cline CLI exposes to Runlayer.

  • Gateway policy (available)

    Every Atlassian call from Cline CLI passes through Runlayer, where your policies can allow, alert, mask, or block it.

  • Audit trail (available)

    Each call is recorded with the user, Cline CLI as the client, the tool, and the policy and scanner decisions.

  • Client hooks (available)

    Capture supported prompts, reasoning, local and MCP tool calls, responses, and scanner decisions in real time.

  • Stop a call before it runs (available)

    Runlayer can deny a tool call before Cline CLI runs it.

  • Block output after it runs (not available)

    Cline CLI ignores Runlayer after a tool runs, so Runlayer cannot block its output. The gateway still applies policy to the call.

  • Redact output in place (not available)

    Runlayer cannot mask tool output in Cline CLI. The gateway still applies policy to the call.

In Cline CLI

  • If Runlayer’s hook times out or crashes, Cline CLI lets the tool call through.
  • This covers the Cline CLI, not the Cline extension for VS Code.

Frequently asked questions

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