[doc] Add section to README on non-flat directory structures for pojects

[fabianhjr]

I was attempting to use sbt in file("path") but in a weird way which was giving me the following error:

java.util.NoSuchElementException: key not found: JVMPlatform
    at scala.collection.MapLike.default(MapLike.scala:236)
    at scala.collection.MapLike.default$(MapLike.scala:235)
    at scala.collection.AbstractMap.default(Map.scala:65)
    at scala.collection.MapLike.apply(MapLike.scala:144)
    at scala.collection.MapLike.apply$(MapLike.scala:143)
    at scala.collection.AbstractMap.apply(Map.scala:65)
    at sbtcrossproject.CrossProject.$anonfun$dependsOn$7(CrossProject.scala:45)
    at sbtcrossproject.CrossProject.$anonfun$mapProjectsByPlatform$1(CrossProject.scala:111)
    at scala.collection.TraversableLike.$anonfun$map$1(TraversableLike.scala:286)
    at scala.collection.immutable.Map$Map3.foreach(Map.scala:376)
    at scala.collection.TraversableLike.map(TraversableLike.scala:286)
    at scala.collection.TraversableLike.map$(TraversableLike.scala:279)
    at scala.collection.AbstractTraversable.map(Traversable.scala:108)
    at sbtcrossproject.CrossProject.mapProjectsByPlatform(CrossProject.scala:110)
    at sbtcrossproject.CrossProject.dependsOn(CrossProject.scala:44)

I think this doc addition might help others get started with more complex build structures.

Thanks @armanbilge for the help on Typelevel's Discord!