How to support multiple Scala versions in a library

Most of this is well supported in sbt within a single source tree

Version specific source directories are usually not need. Scala programs tends to be source compatible – so often in fact that
crossbuilding (http://www.scala-sbt.org/release/docs/Detailed-Topics/Cross-Build) has first class support in sbt.

If you really need version specific code, you can add extra source folders.
Putting this in your build.sbt file will add “src/main/scala-[scalaVersion]” as a source directory for each version as you crossbuild in addition to the regular “src/main/scala”.
(there is also a plugin available for generating shims between version, but I haven’t tried it – https://github.com/sbt/sbt-scalashim)

unmanagedSourceDirectories in Compile <+= (sourceDirectory in Compile, scalaVersion){ (s,v) => s / ("scala-"+v) }

version specific source jars – see crossbuilding, works out of the box

integrated deployment – https://github.com/sbt/sbt-release (has awesome git integration too)

Maven end-users – http://www.scala-sbt.org/release/docs/Detailed-Topics/Publishing.html

Shaded – I have used this one https://github.com/sbt/sbt-assembly which have worked fine for my needs.
Your problem with the assembly plugin can be solved by rewriting the generated pom.
Here is an example ripping out joda-time.

pomPostProcess := {
    import xml.transform._
    new RuleTransformer(new RewriteRule{
        override def transform(node:xml.Node) = {
            if((node \ "groupId").text == "joda-time") xml.NodeSeq.Empty else node
        }
    })
}

Complete build.sbt for for reference

scalaVersion := "2.9.2"

crossScalaVersions := Seq("2.9.2", "2.10.0-RC5")

unmanagedSourceDirectories in Compile <+= (sourceDirectory in Compile, scalaVersion){ (s,v) => s / ("scala-"+v) }

libraryDependencies += "joda-time" % "joda-time" % "1.6.2"

libraryDependencies += "org.mindrot" % "jbcrypt" % "0.3m"

pomPostProcess := {
    import xml.transform._
    new RuleTransformer(new RewriteRule{
        override def transform(node:xml.Node) = {
            if((node \ "groupId").text == "joda-time") xml.NodeSeq.Empty else node
        }
    })
}