Answer for:

How to Clone a single application

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only a certain type of program can be successfully cloned. these are usually small executibles, like utilities and old dos programs.

these programs usually comprise of one or two files and don't make entries into the registry hive.

but overall it is not possible, especially if they require a product key to activate which prevents anti piracy.

another reason is that there can be thousands of registry entries (through out the hive and sometimes with encrypted key names) made during setup by a program.

another reason is that during setup, some of the files being installed are actually being re-programmed / customized for the exact computer its going to work on.