mcp-atlassian: Copilot coding agent retrieves 0 tools from Docker MCP server

Question

When mcp-atlassian (ghcr.io/sooperset/mcp-atlassian:latest) runs as a Docker stdio MCP server in GitHub Copilot Coding Agent on Linux, the log says "Successfully retrieved 0 tools from client: jira-api" even though the server starts and works locally, and another MCP server in the same config (notion-api) lists its tools fine. How do you get the tools to load?

Originally asked on GitHub: https://github.com/sooperset/mcp-atlassian/issues/541

AgentArmor team · Accepted Answer

Status: still open in the mcp-atlassian repo as of November 2025. The thread points to an interop problem between some third-party clients (GitHub Copilot Coding Agent, Warp) and servers launched over Docker stdio; no project-side fix is confirmed, but two workarounds were reported.

**What fixed it for other users**

1. One commenter fixed it by updating FastMCP to a newer version — mcp-atlassian then worked with the GitHub coding agent.
2. Another user put mcp-atlassian behind the TBXark/mcp-proxy remote MCP proxy and reported that resolved the 0-tool retrieval.
3. A Warp user got it working by switching to streamable-http instead of stdio:

```
docker run -p 9000:9000 ghcr.io/sooperset/mcp-atlassian:latest \
  --transport streamable-http --port 9000 --host 0.0.0.0
```

with the client config:

```json
{
  "mcpServers": {
    "mcp-atlassian": {
      "url": "http://localhost:9000/mcp"
    }
  }
}
```

Note that a Copilot user who tried the same streamable-http approach still got 0 tools, so results vary by client.

**What did not help**

- The original reporter ran the Docker stdio config with JIRA_URL, JIRA_USERNAME, JIRA_API_TOKEN and READ_ONLY_MODE passed as env; Copilot connected but retrieved 0 tools while a notion MCP in the same config worked.
- Another user put the token directly in JIRA_API_TOKEN and enabled ENABLED_TOOLS, MCP_VERBOSE and MCP_VERY_VERBOSE for debugging; Copilot still fetched 0 tools.
- A Warp user confirmed the MCP Inspector lists tools correctly, which suggests the server itself responds and the problem is in how some clients call tools/list.

General advice: reproduce with the MCP Inspector first to confirm whether the issue is client- or server-side, keep READ_ONLY_MODE on, and prefer storing the API token in the Copilot environment over hardcoding it in the MCP config.

AgentArmor team · Answer

**What a GitHub user tried on GitHub** (Didn't work)

Ran mcp-atlassian via `docker run -i` with JIRA_URL, JIRA_USERNAME, JIRA_API_TOKEN and READ_ONLY_MODE set in the Copilot MCP config. Copilot connected but logged "Successfully retrieved 0 tools", while a notion MCP in the same config listed its tools.

Source: https://github.com/sooperset/mcp-atlassian/issues/541

AgentArmor team · Answer

**What @villelahdenvuo tried on GitHub** (Worked)

Updated FastMCP to a newer version. The commenter reported this fixed the issue and mcp-atlassian then worked with the GitHub coding agent.

Source: https://github.com/sooperset/mcp-atlassian/issues/541#issuecomment-3561711929

AgentArmor team · Answer

**What @JoolsHattey tried on GitHub** (Worked)

Put mcp-atlassian behind the TBXark/mcp-proxy remote MCP proxy. The user reported this fixed the 0-tool retrieval.

Source: https://github.com/sooperset/mcp-atlassian/issues/541#issuecomment-3528135151

AgentArmor team · Answer

**What @davidstevenrojas tried on GitHub** (Worked)

Started the container with `--transport streamable-http --port 9000 --host 0.0.0.0` and connected the client to `http://localhost:9000/mcp`. The user called it a workaround but confirmed it worked in Warp.

Source: https://github.com/sooperset/mcp-atlassian/issues/541#issuecomment-3270628973

AgentArmor team · Answer

**What @villelahdenvuo tried on GitHub** (Didn't work)

Tried the same streamable-http transport from GitHub Copilot Coding Agent. The server started, but Copilot still reported "Successfully retrieved 0 tools".

Source: https://github.com/sooperset/mcp-atlassian/issues/541#issuecomment-3527743439

mcp-atlassian: Copilot coding agent retrieves 0 tools from Docker MCP server

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mcp-atlassian: Copilot coding agent retrieves 0 tools from Docker MCP server

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