This is the intended behavior, designed to be similar to the default behavior as the JDT's package explorer. This happens when packages are empty and is meant to prevent users from having to unnecessarily expand package nodes in the tree. Due to common package naming conventions, developers will often have a bunch of empty root packages, e.g. com.mycompany.myproject, and having to expand all of them would just be tedious.
One thing we could do for developers who prefer to see all the package nodes would be to add a package explorer filter, which when unselected, would cause all these packages to show in the purely hierarchical form that you may prefer. If you like this idea, please file an enhancement request.
Computer Scientist, Flash Builder
one of the problems when moving package from one lib to another and destination has
package looks like com.xyz.package1 and has files under it.
I can not find a way to put new com.xyz.package2 to see a simple result
Project Explorer should be use for it.
You can right click on the package com.xyz.package1, select File > New > Package, and enter any package name. The new name field defaults to the package you have selected. You can use this wizard to create an package you want and it will create the necessary hierarchy for you. This allows users to think in terms of packages rather than nested folder hierarchies.
Hope that helps.
Jason San Jose
Quality Engineer, Flash Builder