Fix dependency tracing for fewerPreprocessingHoles

Previously, dependency tracing in `ite_removal.cpp` was only done with
the `unsatCores` option but `fewerPreprocessingHoles` requires
dependencies, too. This lead to errors during proof construction when
`fewerPreprocessingHoles` was active. This commit fixes the condition
and includes a test case that previously failed.  Additionally, it fixes
a similar issue in the theory engine.

NOTE: this commit might not fix all instances of this problem.
`smt_engine.cpp` turns certain flags off with `unsatCores`.
Compatibility between those flags and `fewerPreprocessingHoles` needs to
be checked separately.

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