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Re-activate user guide samples integration tests

- Adjusted expected output according to new console

- Updated 'jacoco' and 'source set' samples to not use deprecated API

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Reverted my last fixes to failing tests / refactorings. Apparently, I cannot change the *.out files because they are presented into the manual

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Removed the hack with 1 secs turned into a regex. Now it's using the simple regex mechanism I introduced in previous commit

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Renamed subprojects/gradle-(.+) to subprojects/$1

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  1. … 6178 more files in changeset.