Connect Atlassian to Codex
Give Codex governed access to Atlassian’s 96 tools through Runlayer, with identity, policy, scanning, and audit on every call.
Set up
Add Atlassian to Codex in four steps
Admins approve the server once. Everyone in Codex then gets it through the same governed connection.
- 1
Approve Atlassian in Runlayer
Add Atlassian from the catalog and choose who can use it and which of its tools are allowed.
- 2
Connect Codex to Runlayer
Runlayer’s CLI adds the Runlayer Plugin to Codex’s local plugin marketplace, and users then enable it in Codex. With direct tool listing turned on for your deployment, Atlassian’s 96 tools show up in Codex’s own tool list (Codex 0.122 or newer, installed through the Runlayer CLI).
Codex setup guide - 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
Use Atlassian from Codex
Atlassian’s approved tools appear in Codex. Every call is checked against policy and recorded.
Tools
96 Atlassian tools in Codex
Runlayer policy decides which of these Codex 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.
Control
What Runlayer can see and stop in Codex
Some controls apply to every client at the gateway. Others depend on what Codex exposes to Runlayer.
Gateway policy (available)
Every Atlassian call from Codex passes through Runlayer, where your policies can allow, alert, mask, or block it.
Audit trail (available)
Each call is recorded with the user, Codex 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 or permission request before Codex runs it.
Block output after it runs (available)
Runlayer can block a tool’s output before Codex’s model sees it.
Redact output in place (not available)
Codex cannot take masked output, so Runlayer can block a tool’s output but not mask it. The gateway still applies policy to the call.
Frequently asked questions
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