There are number of ways of achieving results results.
1) As told by Gabriel
2) Don't include -srd switch to harvest root directory as element.
3) use -var in Heat and -d in candle.
e.g for 3
heat.exe dir "$(SolutionDir)MyProject\MyDirectory" -ag -sfrag -srd -var
"var.MyProjectDir" -out  $(ProjectDir)HarvestedFiles.wxs"* 

candle.exe -dMyProjectDir="$(SolutionDir)MyProject\MyDirectory"
$(ProjectDir)HarvestedFiles.wxs



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