Databases missing after exporting server and rebuilding master DB
I have all Databases (mdf and ldf files) in this folder D:\Microsoft SQL Server\MSSQL12.MSSQLSERVER\MSSQL\DATA how to restore them and not lose all functionality?

When you rebuild master, it loses track of where the user databases are.  You just need to attach them, and recreate the logins for any orphaned users.
And also consider linked servers, scheduled jobs and everything else which is stored outside the user databases and was scratched by the rebuild.