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 am try to pass the PAT via headers to my mcp-atlassian container with below config (using langchain-mcp-adapter 0.1.7)

If i put the PAT inside container env, it works

{
  "mcpServers": {
    "mcp-jira": {
      "url": "https://my-mcp-endpoint/mcp",
      "headers": {
        "Authorization": "Token MT...masked...J/"
      },
      "transport": "streamable_http"
    }
  }
}

Steps to Reproduce

try to reach the mcp, with the container log below

25-07-01T06:25:35.911385158Z DEBUG - mcp-atlassian.server.main - UserTokenMiddleware.dispatch: Comparing request_path='/mcp' with mcp_path='/mcp'. Request method='POST'
DEBUG - mcp-atlassian.server.main - UserTokenMiddleware: Path='/mcp', AuthHeader='Toke01J/', ParsedToken(masked)='MTUx01J/', CloudId='None'
2025-07-01T06:25:35.911457142Z DEBUG - mcp-atlassian.server.main - UserTokenMiddleware: No cloudId header provided, will use global config
2025-07-01T06:25:35.911500710Z DEBUG - mcp-atlassian.server.main - UserTokenMiddleware: MCP-Session-ID header found: 3d377ecb7c784840bf98e4ee6bd57c8d
2025-07-01T06:25:35.911522432Z DEBUG - mcp-atlassian.server.main - UserTokenMiddleware.dispatch: PAT (Token scheme) extracted (masked): ...MTUxOTg2**********************xPbm01J/
DEBUG - mcp-atlassian.server.main - UserTokenMiddleware.dispatch: Set request.state for PAT auth.
DEBUG - mcp-atlassian.server.main - UserTokenMiddleware.dispatch: EXITED for request path='/mcp'
INFO: 10.42.79.162:45950 - "POST /mcp HTTP/1.1" 307 Temporary Redirect
2025-07-01T06:25:35.915983928Z DEBUG - mcp-atlassian.server.main - UserTokenMiddleware.dispatch: ENTERED for request path='/mcp/', method='POST'
DEBUG - mcp-atlassian.server.main - UserTokenMiddleware.dispatch: Comparing request_path='/mcp' with mcp_path='/mcp'. Request method='POST'
2025-07-01T06:25:35.916013645Z DEBUG - mcp-atlassian.server.main - UserTokenMiddleware: Path='/mcp/', AuthHeader='Not Provided', ParsedToken(masked)='Not Provided', CloudId='None'
2025-07-01T06:25:35.916028298Z DEBUG - mcp-atlassian.server.main - UserTokenMiddleware: No cloudId header provided, will use global config
2025-07-01T06:25:35.916050528Z DEBUG - mcp-atlassian.server.main - UserTokenMiddleware: MCP-Session-ID header found: 3d377ecb7c784840bf98e4ee6bd57c8d
2025-07-01T06:25:35.916073544Z DEBUG - mcp-atlassian.server.main - No Authorization header provided for /mcp/. Will proceed with global/fallback server configuration if applicable.
DEBUG - mcp.server.streamable_http_manager - Session already exists, handling request directly
2025-07-01T06:25:35.917017860Z DEBUG - mcp-atlassian.server.main - UserTokenMiddleware.dispatch: EXITED for request path='/mcp/'
2025-07-01T06:25:35.917082786Z INFO: 10.42.79.162:45960 - "POST /mcp/ HTTP/1.1" 200 OK
DEBUG - mcp.server.lowlevel.server - Received message: <mcp.shared.session.RequestResponder object at 0x7fbb1165d240>
2025-07-01T06:25:35.917580505Z INFO - mcp.server.lowlevel.server - Processing request of type ListToolsRequest
2025-07-01T06:25:35.917603985Z DEBUG - mcp.server.lowlevel.server - Dispatching request of type ListToolsRequest
DEBUG - mcp-atlassian.server.main - _main_mcp_list_tools: read_only=False, enabled_tools_filter=None
2025-07-01T06:25:35.917799817Z DEBUG - mcp-atlassian.server.main - Aggregated 42 tools before filtering: ['jira_get_user_profile', 'jira_get_issue', 'jira_search', 'jira_search_fields', 'jira_get_project_issues', 'jira_get_transitions', 'jira_get_worklog', 'jira_download_attachments', 'jira_get_agile_boards', 'jira_get_board_issues', 'jira_get_sprints_from_board', 'jira_get_sprint_issues', 'jira_get_link_types', 'jira_create_issue', 'jira_batch_create_issues', 'jira_batch_get_changelogs', 'jira_update_issue', 'jira_delete_issue', 'jira_add_comment', 'jira_add_worklog', 'jira_link_to_epic', 'jira_create_issue_link', 'jira_create_remote_issue_link', 'jira_remove_issue_link', 'jira_transition_issue', 'jira_create_sprint', 'jira_update_sprint', 'jira_get_project_versions', 'jira_get_all_projects', 'jira_create_version', 'jira_batch_create_versions', 'confluence_search', 'confluence_get_page', 'confluence_get_page_children', 'confluence_get_comments', 'confluence_get_labels', 'confluence_add_label', 'confluence_create_page', 'confluence_update_page', 'confluence_delete_page', 'confluence_add_comment', 'confluence_search_user']
DEBUG - mcp_atlassian.utils.tools - Including tool 'jira_get_user_profile' because enabled_tools filter is None.
2025-07-01T06:25:35.917847037Z DEBUG - mcp-atlassian.server.main - Excluding Jira tool 'jira_get_user_profile' as Jira configuration/authentication is incomplete.

I enable MCP_VERY_VERBOSE, the container log as above, that it shows configuration/authentication is incomplete. the token extracted (which is masked) inside the log, seems correct.

Expected Behavior

the mcp not suppose to show configuration/authentication is incomplete.

Actual Behavior

the container log show `configuration/authentication is incomplete.` when I try to pass the PAT from header

mcp-atlassian Version

0.11.9

Installation Method

Docker

Operating System

Other

Python Version

3.13

Atlassian Instance Type

Jira Server / Data Center

Client Application

langchain-mcp-adapter 0.1.7

Additional Context

No response