[Bug]: MCP Atlassian Server Fails to Handle Tool Invocations

[Zakky709]

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

The mcp-atlassian server (v0.11.9) successfully connects to Claude Code and initializes, but fails to execute any Jira API operations. All tool invocations return either errors or empty results, despite valid credentials that work with direct API calls.

Steps to Reproduce

1. Configure mcp-atlassian with valid credentials:

claude mcp add atlassian "uvx mcp-atlassian --jira-url https://moneyforward.atlassian.net --jira-username user@example.com --jira-token YOUR_TOKEN"

2. Verify the server connects (shows "✓ Connected" in claude mcp list)

3. Try to use any Jira tool through Claude Code MCP:

   • jira_get_issue with a valid issue key returns "Error calling tool 'get_issue'"
   • jira_search with any JQL returns {"total": -1, "start_at": -1, "max_results": -1, "issues": []}
   • jira_get_all_projects returns empty array []

Expected Behavior

The tools should return actual data from Jira, as the same credentials work perfectly with direct curl commands:

curl -u "user@example.com:TOKEN" \
  -X GET -H "Accept: application/json" \
  "https://moneyforward.atlassian.net/rest/api/3/myself"
# Returns valid user data

curl -u "user@example.com:TOKEN" \
  -X GET -H "Accept: application/json" \
  "https://moneyforward.atlassian.net/rest/api/3/issue/ISSUE-123"
# Returns valid issue data

Actual Behavior

## Actual Behavior
- Server initializes successfully and reports capabilities
- All tool invocations fail with either generic errors or empty/default responses
- The `-1` values in search responses suggest error defaults rather than actual API responses

mcp-atlassian Version

0.11.9

Installation Method

From PyPI (pip install mcp-atlassian / uv add mcp-atlassian)

Operating System

macOS

Python Version

3.13.3

Atlassian Instance Type

Jira Cloud

Client Application

CLI / Claude Code

Additional Context

No response