You configure permissions differently based on whether you extract metadata from packages in the Microsoft SQL Server repository or from packages in package files.
If you extract metadata from packages in the repository, configure permissions for the Windows user who starts the Metadata Manager Agent. The Metadata Manager Agent uses Windows authentication to connect to SQL Server Integration Services. The Windows user who starts the Metadata Manager Agent must have read permission on the objects that the Metadata Manager Agent extracts.
If you extract metadata from package files and you configure Metadata Manager to use the latest source files or you specify a source directory, the Windows user who starts the Metadata Manager Agent must have read permission on the files and on the directory that contains the files.