[BUG] "com.atlassian/atlassian-mcp-server installation failed" during `apm install`

[bgrainger]

Describe the bug
apm can find the Atlassian MCP server but the suggested installation instructions fail when running apm install.

To Reproduce

Create apm.yml with the following content:

dependencies:
  apm: []
  mcp:
  - com.atlassian/atlassian-mcp-server

Run apm install --verbose:

❯ apm install --verbose
[>] Installing dependencies from apm.yml...
Parsed apm.yml: 0 APM deps, 1 MCP deps
No APM dependencies found in apm.yml
+- MCP Servers (1)
No scripts detected, using all installed runtimes: copilot, vscode
Validating 1 registry servers...
Installing 1 servers...
|  >  com.atlassian/atlassian-mcp-server
|     +- Configuring for Copilot, Vscode...
Configuring copilot...
  Installing com.atlassian/atlassian-mcp-server...
  com.atlassian/atlassian-mcp-server already configured, skipping
Configuring vscode...
  Installing com.atlassian/atlassian-mcp-server...
Unable to configure server: com.atlassian/atlassian-mcp-server
  x com.atlassian/atlassian-mcp-server installation failed
  x Failed to install com.atlassian/atlassian-mcp-server
|  +  com.atlassian/atlassian-mcp-server -> Copilot, Vscode (configured)
+- Configured 1 server

[*] Installed 1 MCP server.

It "Failed to install com.atlassian/atlassian-mcp-server" for VS Code. Nothing is written to .vscode/mcp.json.

Expected behavior
.vscode/mcp.json should be updated with something like:

  "Rovo": {
    "type": "http",
    "url": "https://mcp.atlassian.com/v1/mcp",
    "headers": {}
  },

Environment (please complete the following information):

• OS: Windows 11
• Python Version: None (No system-wide installation; I use uv for everything)
• APM Version: 0.8.11
• VSCode Version (if relevant): 1.115.0

Logs

Additional context

MCP details were obtained through apm mcp search and apm mcp show so it was expected that using the values it printed would "just work".

❯ apm mcp search atlassian

MCP Registry Search
Query: atlassian

+ Found 1 MCP server
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━┓
┃ Name                               ┃ Description               ┃  Latest  ┃
┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━┩
│ com.atlassian/atlassian-mcp-server │ Atlassian Rovo MCP Server │    --    │
└────────────────────────────────────┴───────────────────────────┴──────────┘

 Use apm mcp show <name> for detailed information

❯ apm mcp show com.atlassian/atlassian-mcp-server

MCP Server Details
Fetching: com.atlassian/atlassian-mcp-server
           MCP Server: com.atlassian/atlassian-mcp-server
┏━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Property     ┃ Value                                             ┃
┡━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
│ Name         │ com.atlassian/atlassian-mcp-server                │
│ Version      │ 1.1.1                                             │
│ Description  │ Atlassian Rovo MCP Server                         │
│ Repository   │ https://github.com/atlassian/atlassian-mcp-server │
│ Registry ID  │ 87fafa74...                                       │
└──────────────┴───────────────────────────────────────────────────┘
                                Remote Endpoints
┏━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━┓
┃ Type       ┃ URL                                      ┃ Features             ┃
┡━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━┩
│            │ https://mcp.atlassian.com/v1/mcp         │ Hosted by provider   │
│            │ https://mcp.atlassian.com/v1/sse         │ Hosted by provider   │
└────────────┴──────────────────────────────────────────┴──────────────────────┘
                                   * Installation Guide
┏━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Step  ┃ Action                         ┃ Command/Config                                 ┃
┡━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
│ 1     │ Add to apm.yml dependencies    │ mcp: - com.atlassian/atlassian-mcp-server      │
│ 2     │ Install dependencies           │ apm install                                    │
│ 3     │ Direct install (coming soon)   │ apm install com.atlassian/atlassian-mcp-server │
└───────┴────────────────────────────────┴────────────────────────────────────────────────┘

[bgrainger]

The linked PR showed me that the following syntax can be used as a workaround:

dependencies:
  apm: []
  mcp:
  - name: Atlassian
    registry: false
    url: https://mcp.atlassian.com/v1/mcp
    transport: http