Always Allow option not persisted for MCP server tools

Extension version: 1.92.0.0
Visual Studio: 18.5.2

I can change an MCP Server's tool to Always Allow, and it will stop requiring me to press `Run >` every time I want to execute the tool.

Once I do this, I can load a Jira work item during the current session. It even adds entries to the `default.json` file:
```
"tools": [
"@jira"
],
"toolAliases": {},
"allowedTools": [
"@jira/jira_get_issue"
],
```

This is great, and extremely handy. I can ask Amazon Q to "tell me about " and it will call `jira_get_issue`. When I go back to the jira mcp server configuration panel when you go back to it, `jira_get_issue` shows as "Always allow"

Awesome.

_Until_ I click the `Refresh MCP Servers` button. Or _Until_ I restart Visual Studio.

Then reload the permission has changed back to "Ask", even though it still works in my current session.

Everything is still correct in `default.json` but `jira_get_issue` reverts to the annoying `Cancel | Run >` prompt.

It looks like the setting is getting written properly to `default.json` when changing to "Always allow" in the config panel, but it's not being read when reading back from `default.json`. This read would happen both when starting VS and when refreshing the mcp servers.

So, to summarize the issue, `allowedTools` is not read properly from `default.json`.

Start by tracing how the MCP server configuration panel writes and reloads default.json, focusing on the allowedTools entry and the Refresh MCP Servers flow. Reproduce the issue by selecting Always allow, refreshing or restarting Visual Studio, and checking whether the permission is restored from default.json. Done means the setting remains Always allow after both refresh and restart.

Written by the indexing model from the issue text.