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Prune directories should not be default for update and checkout. Undesirable pruning occurs, such as pruning the "test" directory of a project when the test directory is empty (test packages haven't been written yet).
In other cases, the prunning must be used (e.g. you will not be able to compile NetBeans sources of checked out without prune). I'm afraid we'll not be able to fix this while satisfy all users. Perhaps we should present this option also in the non-advanced mode. This is similar to update and it's -d and -P options.
Is not it possible to set an user default? I mean by running advanced mode then disable pruning and pushing [Set as Default]. User could also edit profile but it's not viable alternative.
Counter issue #52889. My proposed fix is to streamline implementation of defaults. Replace [next] [prev] [set default] [use default] < actual dialog content > [cancel] [ok] with < actual dialog content > [set as default] [cancel] [ok] where [set as default] *persists* actual value. The default value is automatically loaded next time command is invoked. My proposed fix includes UI change, eliminating useless controls. This elimination 'highlights' remaining controls. Jano, do you see any blocker from your side?
UI updated, now waiting one week for VcsCommandsProvider SPI enhancement review. The proposed SPI change allows to create unique command IDs.
41425 is more generic issue covering this one, *** This issue has been marked as a duplicate of 41425 ***