Issues with creating assessment.md

### Description

## Issue

While running the .NET migration agent (1.0.1037-preview1), the assessment.md could not be generated using the "generate_dotnet_upgrade_assessment" tool. Instead, the agent created the assessment.md from its current chat context.

Here is the error that was shown at the top of the assessment.md.

> Payroll.Mvc to Payroll.MvcCore (.NET 10) Gap Assessment
> Manual fallback assessment.
> generate_dotnet_upgrade_assessment ran but did not create assessment.md in this scenario folder, so this file was populated from the validated gap analysis to keep the workflow moving.

## Steps to Reproduce
1. Updated modernize-dotnet to 1.0.1037-preview1
2. Ran Github Copilot CLI
3. Switched to modernize-dotnet agent, and ensured appropriate skills / MCP servers etc were loaded
4. Asked the agent to analyse our project for migrating from .NET framework to .NET 10 and give me a summary of what is needed.
5. After the agent provided a summary, I asked agent to continue with the migration process
6. Agent tried creating the assessment.md, but continuously failed, until the agent suggested to create the assessment.md from the knowledge in step 5.

## Expected Behavior
A generated assessment.md without error.

## Desktop/Environment:
- OS: [e.g. Windows 11]
- Environment: Github Copilot CLI v1.0.34
- Model: I think it was GPT 5.4, but could have been 5.3 Codex
- Version: 1.0.1037-preview1