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Hello Guillaume,
Source Control's function is to create a representation of all of the objects in a schema as a series of scripts - so they will always be CREATE statements. If you need to make a synchronization script that alters objects, you can use Schema Compare for Oracle to compare the folder of CREATE scripts to a database or another folder and go through the synchronization wizard to make the script.
Hope this helps.
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Is it possible to have the tables changes checked-in as "ALTER TABLE" in the same script instead of a complete "CREATE TABLE".
Thanks,
Guillaume