MSM is a Windows Installer standard, wixlib is not.  Otherwise they are 
similar in function with wixlib being lighter weight and more flexible.

But your scenario confuses me.  An MSI can install one and only one 
product.  It would be more accurate to say   the files for one feature goes 
in M1 and the files for another feature go in M2.  Unless you are really 
talking about patches, a new MSI is always going to have both M1 and M2.

Either you stick with this monolithic design or you look at creating 2 
MSI's and using Burn to chain them together.

----------------------------------------
 From: "Jan Kucera" <t-j...@microsoft.com>
Sent: Thursday, March 14, 2013 6:29 AM
To: "wix-users@lists.sourceforge.net" <wix-users@lists.sourceforge.net>
Subject: [WiX-users] Merge modules & wixlib compatibility

Hello,
I am trying to move from merge modules to wixlibs, but I am not sure 
whether all the functionality is preserved.

Consider the following scenario:
- one product goes into the merge module M1
- other product goes into the merge module M2
- a MSI is created containing both M1 and M2 and installed
- the first product gets some important fix
- new MSI is created just having the fixed M1

Now if I understand correctly, the installer correctly upgrades the M1 
install with this MSI. Later when there is a new version of the whole 
product, it will correctly upgrade both fixed M1 and original M2. That is 
the case also when the M1 only MSI is installed first.

Now does this work even when I switch from modules to wixlibs?
Is there overall any reason why would one need to use merge modules instead 
of wixlib (apart from supporting non-WiX environment)?

Thanks!
Jan
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