We recently encountered this problem as well. There is an old message
(here:
http://www.nabble.com/WebDir-element---no-longer-can-contain-webapplication-tf851560.html#a2280481)
about it. From the IIS MMC, you can make any directory a web application.
In the metabsae, it creates any IISConfigObject elements for the directories
above and then the web directory elements are created with the relevent app
names in them. Does anybody have any information about why the IIS team at
Microsoft says this isn't supported? It seems odd that you can do this in
the IIS MMC, but not in WiX.
Dana
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