Hi,
You did not indicate if this is an upgrade to an existing environment or a fresh install. Either way, the error provided...
Error: Exception encountered in updateTemplateFolders
com.niku.dms.util.DMSException: File is currently checked out by another user.
might indicate problems with Collaboration document templates (this information is created with the XDM install) which are found on the Clarity Admin side...Project Management >> Document Templates.
Try running a query as such: select * from clb_dms_files where lock_owner_id <> 0
This should return zero (0) rows, which would imply that all document templates are checked in.
You might try stopping nsa from the command line, restarting, then running the command: nikuadmin general upload-config to ensure your NSA properties file information is correct in the database. I say this based on your other issues where the document file store and index information might have been corrupted (aka not installed or setup correctly), as you really should verify all NSA settings BEFORE running the various installation component steps (pre-upgrade, database, xdm and post-upgrade).
Let me know how this goes.
Allen Bollinger
CA Technologies
Sr. Services Consultant