I understand there are 2 batch files that need to be run to bring the repository up to 2013 UpgradeRepositories.bat and SetupRepositoryIndices.bat . The upgrade batch file bombs for me immediately looks like it may be a permissions problem. Before I go there is there something I may be missing, like what should my current directory be when I execute.
Another alternative is to use Package Management in MapAdmin ( http://servername/mapserver2013/mapadmin/login.php
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I am having the same permission problems with upgrading from AIMS 2012 to 2013 although logged in as admin... done it like discribed here: Link
Is there an other way to backup the user files (Names, ID's, passwords...) ?