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If you are migration from,
1. 9.3.X to any legacy 11.1.1.X - you can perform a schema migraion and laso you can leverage migration utility if you wish to build your mata data structures
manually, with schema migration both Metadata and System meta data will get migrated.
2. 9.3.X or 11.1.1.X to 11.1.2 ( complete web) - you need to do a repository migration, you need to be little patient as it takes more time Legacy to Web
( remember migration utilty will not work from Legacy to Web migration)
3. 11.1.2.X to any latest versions, you can use migration utility as well as schema refresh,
wish it helps!
The metadata utility will only migrate the metadata configuration, not the versions themselves. To upgrade the respository on older versions you should restore the database schema as you have done and then run the update scripts. Look in the "Oracle Update Scripts" folder. There are sql scripts provided for updating the database from various versions.