Currently the References element isn't able to specify different file names/references based on the target platform.
This should be split up like the depependencies:
<References>
<Group targetFramework="net45">
<Reference file = "blah.dll" />
</group>
<group targetFramework=windows-javascript>
<Reference file="foo.dll" />
<group>
<references>
Possibly with a default group like targetFramework=* as a fallback.
This should be split up like the depependencies:
<References>
<Group targetFramework="net45">
<Reference file = "blah.dll" />
</group>
<group targetFramework=windows-javascript>
<Reference file="foo.dll" />
<group>
<references>
Possibly with a default group like targetFramework=* as a fallback.