Regarding the use of the PAT field in the configuration.json file after migration init is run - for version 11.6.0.0.
It looks like this is not implemented. I am not seeing examples for using the source and target command line options for user, password and domain but putting these in still fails for me so not sure I am using these correctly. I am already authenticated in source and target environments.
The error is:
[10:22:23 ERR] Unable to configure store Microsoft.TeamFoundation.TeamFoundationServerUnauthorizedException: TF30063: You are not authorized to access https://dev.azure.com/xxxxx/. ---> System.Net.WebException: The remote server returned an error: (401) Unauthorized.
The PAT is only used for a small number of calls. Most are implemented using the ObjectModel which is AD Authenticated. In general, the tool will pop authentication boxes, which may have cached credentials.
#1 You should be able to delete the cached credentials in the Windows Credential Manager.
The Username and Password options are only useful when connecting to a local TFS environment on Active Directory and do not, to my knowledge, work with Azure AD.
The tool is supposed to pop an interactive authentication box for connecting to Azure DevOps, however, if you fill out the Username and Password it takes a different path.
I recommend that you Fork the repository, clone it, and open in Visual Studio to run in Debug to see where you are having an issue.
My bet is cached credentials, but it could well be something else.