Alfredo (et al)..
The target schema problem in particular arises when various changes are
individually specified to a test/development environment such that the
resulting changes are consistent.  That 'finished product' database is then
decompiled to produce the relevant schema, which in turn is used as the
target schema.  The schema in that case does reflect where you came from
and where you want to be - but it does NOT reflect what it took to get
there.
There are I'm certain realistic limits to the 'intuitive' retention of
existing data/indices - and far too often standard jcl might be utilized
such that a blanket yes or no answer to a prompt would be part of
that 'canned' process.

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