[Bug]: Orverwritesettings fail with custom Al-Go Template

AL-Go version

9.0

Describe the issue

the "overwriteSettings" setting fails to overwrite if the setting is coming from a Custom Al-Go template.

Expected behavior

"overwriteSettings" will overwrite a setting instead of it being merged.

Steps to reproduce

1. Create a new Custom AL-Go-template from https://github.com/microsoft/AL-Go-AppSource.
2. Create a new repository from the template Repo-A
3. in the new template - add appDependencyProbingPaths for Repo-A intp .AL-Go/settings.json
4. update both repository's in order template --> Repo-A
   Repo-A should now have a probing path in .github/AL-Go-TemplateProjectSettings.doNotEdit-json

.6 in Repo-A add into .github/AL-Go-Settings.json
"appDependencyProbingPaths"
], "appDependencyProbingPaths": [
]

when CI/CD is running for Repo-A appDependencyProbingPaths is merged instead of being overwritten

Additional context (logs, screenshots, etc.)

The reason for this weird setup is that our custom template contains functionality that is common for all of ours app-source repository's including Repo-A.
Else we will need to have 2 Custom AL-Go template to maintain with the same code/ functionality

Compare the settings in .AL-Go/settings.json, .github/AL-Go-TemplateProjectSettings.doNotEdit-json, and .github/AL-Go-Settings.json while running the described CI/CD workflow. Start by tracing how appDependencyProbingPaths from the custom template is combined with repository settings. Done means an explicit repository value in AL-Go-Settings.json replaces the template value instead of being merged.