A. Prior to App-V 4.6 SP1, when an application was sequenced, you had to launch the applications outside of the App-V sequencer to perform initial configuration tasks and let the application perform any initial setup. The sequencer would then assess what parts of the virtual application should be in feature block 1, and therefore sent to the client prior to the application launching.
The App-V 4.6 SP1 sequencer has a large number of improvements, making it far easier to sequence applications. You're no longer required to run applications outside of the sequencer, thanks to this step being built into the sequencer. During the Configure Software step, all applications will be shown, and can be run to perform the initial configuration.
Later in the process, during the Customer, Streaming step, applications are launched to evaluate which part of the content of the virtualized application should in Feature Block 1.