Software Deployment

1) Assuming the EXE doesn't extract and execute an MSI, capture it to one. If it does (check the %TEMP% or %APPDATA% folder for new folder(s) and an MSI when the EXE presents its first screen), create a transform for the MSI.

What do you mean by 'disabling' of shortcuts? What's the point of having a shortcut if it's disabled?!?

2) Why would you want self-healing to occur every time the application is launched? For more on self-heaing, Google John McFadyen's blog on the subject.

3) A spectacularly bad idea. How will you deal with an update or patch to one of those applications?

Before you do anything else, though, Google for the excellent e-book by Phil Wilson, The Definitive Guide To Windows Installer. Read and digest. You will struggle with packaging anything beyond basic applications unless you know and understand the fundamentals.

i am asking this questions for practice iam still in learning 

how to shake a hornets nest....

IF you have an exe and its an EXE, you need to either from scratch, build an MSI with all the settings (that you don't really know about) so, use a tool to capture what the exe does and spit out an MSI.

Once you have the MSI, you are in charge (if its a vendor MSI, you are only half in charge, all changes with an MST)

merging apps into one MSI.... don't.
Ever, I mean, just don't.

But you are going to want to know why... and one day you will ignore this information and put 4 apps together.

4 apps will have at least 4 different development cycles. When an update comes out for one app, you will make the change, roll it out, then 6 weeks later another app will change, you make the change roll it out etc.

1 app, 1 MSI. life is simpler.

Exceptions to the rule..

I have seen places that have 'packaged' something like, BG info (with its cfg file) AND an INI file (unrelated to BG info) and say, an in house 'choose my printer' exe. Wrapped it all up into ONE MSI, there by breaking the rule.

why??? who knows, but their logic was, BGinfo wont change, nor will the config, on the other INI file, and the choose printer thing has not changed in years...
(you may be interested to know that it worked out OK for them)

but since your learning, DONT do it.

1. You can delete shortcuts from an MSI using a transform. The MSI is unchanged, so the shortcuts remain available if you need them, just by deleting the transform and creating a new one.

2. Reading the information that John McFadyen has published in his blog. Constant self healing is a sign of a faulty package so don't go that route.

3. Would you want to learn about amputation by cutting off your arm?  Merging MSIs into one is truly a spectacularly bad idea and it is something you should avoid like ebola. There is really nothing to be learned here.  However, your question suggests you have not downloaded the Windows Installer SDK, part of the Microsoft Platform SDK, as this provides additional MSI resources. Also google for the MSI.CHM help file which is no longer in the current SDK but is still a valuable resource when packaging MSI files.