I was able to skip deploying webconfig on root folder by following approach MsDeploy Skip Root Web Config deployment only
However i have another folder containing web.config apart from "views" folder which needs to be negated from skip arguement. I tried following which seems to be incorrect regular expression and didnot work
absolutePath="(?<!Views|Configs)\\Web\.config"
where Configs is the folder containing webconfig file. what should be right one
I got it working by this
absolutePath="(?<!Views)(?<!Configs)\\Web\.config"