[Bug]: Fix NuGet package reference check false-positive issue notifications

[omranatstarion]

What type of issue is this?

• Bug report
• Feature request

Prerequisites

• I have written a descriptive issue title
• I have verified that I am running the latest version of the SysML2.NET
• I have searched open and closed issues to ensure it has not already been reported

Description

The existing NuGet package reference check workflow can create issue notifications even when no real package issue is present.

The main problem is that some checks rely on the generated log file having content. However, commands like dotnet list package --deprecated --include-transitive can still write normal output even when no deprecated packages are found. This can make the workflow mark the check as failed/true incorrectly.

The workflow should only report an issue when real package rows are detected.

Work to do:

• update deprecated package detection to check for actual package result rows instead of checking if the log file is not empty
• make outdated and vulnerable package detection use the same safer matching logic
• avoid creating or updating GitHub issues from pull request runs
• automatically close the existing NuGet package issue when the check becomes clean again
• keep test project results out of the generated issue if they are not relevant for dependency maintenance

Steps to Reproduce

Current behavior can be reproduced by running the existing NuGet package reference check workflow when the package check output contains normal dotnet list package messages but no real package rows.

The workflow may still create or update the NuGet Package Issues Detected issue even though there are no actual deprecated, outdated, or vulnerable packages to report.

System Configuration

• mycelium bloom version: current development version
• Environment (Operating system, version and so on): GitHub Actions runner
• .NET Framework version: .NET 10
• Additional information: This concerns the existing NuGet package reference check workflow.