MCP Tools Not visible by custom agent

[CezaryKlus]

Describe the bug

1. Define a custom agent with tools in MD frontmatter like:

tools: [execute, read, edit, search, web, agent, todo, context7/*, github-mcp-server/*, ado/core_list_projects, ado/search_workitem, ado/wit_get_work_item, ado/wit_list_work_item_comments, ado/wit_get_work_item_type]

2. Observe that it does not see them to see any of the tools (should have used ado tools):

Actually looking at the available tools in this environment, I have: git, curl, gh.

This is repeatable. Model: Claude Sonnet 4.6

This issue shall be reopened: #1200

Affected version

1.0.48

Steps to reproduce the behavior

No response

Expected behavior

No response

Additional context

In the corresponding request however the ado tool was listed:

{
            "defer_loading": true,
            "description": "Get a single work item by ID. If a project is not specified, you will be prompted to select one.",
            "input_schema": {
                "additionalProperties": false,
                "description": "{$schema: \"http://json-schema.org/draft-07/schema#\"}",
                "properties": {
                    "asOf": {
                        "description": "Optional date string to retrieve the work item as of a specific time. If not provided, the current state will be returned.\n\n{format: \"date-time\"}",
                        "type": "string"
                    },
                    "expand": {
                        "description": "Expand options include 'All', 'Fields', 'Links', 'None', and 'Relations'. Relations can be used to get child workitems. Defaults to 'None'. Cannot be used together with the fields parameter.",
                        "enum": [
                            "all",
                            "fields",
                            "links",
                            "none",
                            "relations"
                        ],
                        "type": "string"
                    },
                    "fields": {
                        "description": "Optional list of fields to include in the response. If not provided, all fields will be returned. Cannot be used together with the expand parameter.",
                        "items": {
                            "type": "string"
                        },
                        "type": "array"
                    },
                    "id": {
                        "description": "The ID of the work item to retrieve.\n\n{minimum: 1}",
                        "type": "number"
                    },
                    "project": {
                        "description": "The name or ID of the Azure DevOps project. Reuse from prior context if already known. If not provided, a project selection prompt will be shown.",
                        "type": "string"
                    }
                },
                "required": [
                    "id"
                ],
                "type": "object"
            },
            "name": "ado-wit_get_work_item"
        },