[Bug]: Cannot access Jira/Cofluence when using from docker mcp toolkit

[Dark-Zeus]

Prerequisites

• I have searched the existing issues to make sure this bug has not already been reported.
• I have checked the README for relevant information.

Bug Description

I have installed the MCP server through docker MCP toolkit and added the api keys (cloud) and other configurations. When I try to get infomation through Claude Desktop I get varios errors or empty results. The API key is in "Never Accessed" state in the atlassian page.

Steps to Reproduce

1. Add Atlassian MCP server through Docker MCP Toolkit.
2. Configure the tool using configuration page.
3. Install claude desktop
4. Enable MCP access through docker (MCP toolkit -> clients)
5. Restart Claude Desktop
6. Verify if the "MCP_DOCKER" integration is added and enabled
7. Run any query

Expected Behavior

I get the proper results from the search

Actual Behavior

server responds with empty resultset or various error states

mcp-atlassian Version

0.11.2

Installation Method

Docker

Operating System

Windows

Python Version

3.13.5

Atlassian Instance Type

Jira Cloud

Client Application

Claude Desktop

Additional Context

No response

[gpinkham]

I am getting a similar error and I believe its because Atlassian removed some old APIs but mcp-atlassian is still using them. this is the error message I get:

API request failed: 410 Gone {"errorMessages":["The requested API has been removed. Please migrate to the /rest/api/3/search/jql API. A full migration guideline is available at https://developer.atlassian.com/changelog/#CHANGE-2046"],"errors":{}}

[bartoszgosiewski]

I have similar problem but using n8n. Whenever MCP client node in n8n is trying to access docker's mcp gateway (MCP Toolkit) there seems to be no auth keys used. This results in 0 Tools available to n8n client node. 0 Tools is also visible in mcp-gateways's logs.

[yossi-attas-sb]

Getting similar behavior. No Jira searches succeed and the following logs are showing.

azureuser@slack-app-broker:~/mcp-servers/atlassian$ docker run --rm -p 9000:9000 --env-file .env   ghcr.io/sooperset/mcp-atlassian:latest   --transport sse --port 9000
[09/25/25 15:01:16] INFO     Starting MCP server 'Atlassian MCP'   server.py:783
                             with transport 'sse' on                            
                             http://0.0.0.0:9000/sse                            
INFO - FastMCP.fastmcp.server.server - Starting MCP server 'Atlassian MCP' with transport 'sse' on http://0.0.0.0:9000/sse
ERROR - mcp-jira - Error fetching metadata for JQL 'created >= "2025-09-25"': The requested API has been removed. Please migrate to the /rest/api/3/search/jql API. A full migration guideline is available at https://developer.atlassian.com/changelog/#CHANGE-2046
ERROR - mcp-jira - Error fetching metadata for JQL 'created >= 2025-09-25': The requested API has been removed. Please migrate to the /rest/api/3/search/jql API. A full migration guideline is available at https://developer.atlassian.com/changelog/#CHANGE-2046
ERROR - mcp-jira - Error fetching metadata for JQL 'created >= startOfDay()': The requested API has been removed. Please migrate to the /rest/api/3/search/jql API. A full migration guideline is available at https://developer.atlassian.com/changelog/#CHANGE-2046
ERROR - mcp-jira - Error fetching metadata for JQL 'created >= -7d': The requested API has been removed. Please migrate to the /rest/api/3/search/jql API. A full migration guideline is available at https://developer.atlassian.com/changelog/#CHANGE-2046

With another Jira automation project i have, i had to explicitly migrate from these deprecated API a few weeks back to use the enhanced search endpoint instead.

[gpinkham]

I have this fixed in my local env. just trying to find a spare minute to send up a PR. coming soon I hope