I spent some time working on this issue also.  I focused on my wixlib project
first, then the msi project, and then the bundle project, tracking down the
various reasons as to why I could not do an incremental build.  I resolved
the problems in each level of building before trying to solve the problems
at the next level.  Enabling diagnostic reporting in the build log was
helpful.  (VS2010\Tools\Options\Projects and Solutions\Build and Run).

For me there were several issues.  I had implemented an auto increment which
was changing .wxi files and forcing a rebuild.  I had implemented signing in
the VS Post Build event (as most tutorials suggest), which also voided the
timestamps and causes a rebuild.  Look at implementing you signing in the
SignMsi and related MSBuild targets.  There are examples in the WiX source
code.

Even with these changes, each time I build the bundle, while the Msi project
skips both compiling and linking when there are no changes, the batched
targets for each culture are rebuilt.  So to expedite a development build I
use the Debug configuration and only build two of my supported languages.  I
do this because if I only build one of the supported languages the output
path changes to one which does not include the culture, which messes up the
signing code.  So I build two cultures for development and I use the
'Release' configuration to build all of the cultures.  This as improved my
build times significantly.



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