DoNotUse flags and comments should be copied to new child items

[Nicklas Nordborg]

In wizards with manual selection it is possible to select items with a DoNotUse flag. In most cases the wizard will display a warning but it is allowed to continue. The DoNotUse flag (and comment) should be copied to all new child items that are created.

Note that new child items are created in a lot of places. Luckily the changes made in #1056 should make it easy to find all places since names for new child items are made in a central place. We need to find all places that call ReggieItem.getNextChildItemName() and then add code for copying DoNotUse annotations.

[Nicklas Nordborg]

In 5789:

References #1217: DoNotUse flags and comments should be copied to new child items

Implemented ReggieItem.copyDoNotUseAnnotations() as a helper method to copy DoNotUse annotations from one item to another.

Temporarily marked the current child name generator methods as deprecated to make it easier to find all places where new child items are created (assuming that all places that create child items are using one of the methods).

[Nicklas Nordborg]

In 5790:

References #1217: DoNotUse flags and comments should be copied to new child items

Moved the helper method from ReggieItem.copyDoNotUseAnnotations() to a separate utility class DoNotUse since it easier to use two regular BASE items instead of one ReggieItem and one BASE item.

Fixed the implementation in the Cufflinks, StringTie and VariantCalling pipelines.

[Nicklas Nordborg]

In 5791:

Fixes #1217: DoNotUse flags and comments should be copied to new child items

Should be implemented in all places now.