If you do something like the following:

{{$ sbt
> compile
>...
> clean
>...
> compile}}

you end up with the following error:

{{[trace] Stack trace suppressed: run last daffodil-lib/compile:genProps for the full output.
[error] (daffodil-lib/compile:genProps) Failed to generate code
[error] Total time: 3 s, completed Apr 20, 2016 3:14:58 PM
> last daffodil-lib/compile:genProps
java.lang.RuntimeException: Failed to generate code
at scala.sys.package$.error(package.scala:27)
at DaffodilBuild$.runPropertyGenerator(build.scala:208)
at DaffodilBuild$$anonfun$propgenSettings$1$$anonfun$6.apply(build.scala:195)
at DaffodilBuild$$anonfun$propgenSettings$1$$anonfun$6.apply(build.scala:195)
at sbt.FileFunction$$anonfun$cached$1.apply(Tracked.scala:188)
at sbt.FileFunction$$anonfun$cached$1.apply(Tracked.scala:188)
at sbt.FileFunction$$anonfun$cached$2$$anonfun$apply$3$$anonfun$apply$4.apply(Tracked.scala:202)
at sbt.FileFunction$$anonfun$cached$2$$anonfun$apply$3$$anonfun$apply$4.apply(Tracked.scala:198)
at sbt.Difference.apply(Tracked.scala:177)
at sbt.Difference.apply(Tracked.scala:158)
at sbt.FileFunction$$anonfun$cached$2$$anonfun$apply$3.apply(Tracked.scala:198)
at sbt.FileFunction$$anonfun$cached$2$$anonfun$apply$3.apply(Tracked.scala:197)
at sbt.Difference.apply(Tracked.scala:177)
at sbt.Difference.apply(Tracked.scala:152)
at sbt.FileFunction$$anonfun$cached$2.apply(Tracked.scala:197)
at sbt.FileFunction$$anonfun$cached$2.apply(Tracked.scala:195)
at DaffodilBuild$$anonfun$propgenSettings$1.apply(build.scala:197)
at DaffodilBuild$$anonfun$propgenSettings$1.apply(build.scala:190)
at scala.Function5$$anonfun$tupled$1.apply(Function5.scala:35)
at scala.Function5$$anonfun$tupled$1.apply(Function5.scala:34)
at scala.Function1$$anonfun$compose$1.apply(Function1.scala:47)
at sbt.$tilde$greater$$anonfun$$u2219$1.apply(TypeFunctions.scala:42)
at sbt.std.Transform$$anon$4.work(System.scala:64)
at sbt.Execute$$anonfun$submit$1$$anonfun$apply$1.apply(Execute.scala:237)
at sbt.Execute$$anonfun$submit$1$$anonfun$apply$1.apply(Execute.scala:237)
at sbt.ErrorHandling$.wideConvert(ErrorHandling.scala:18)
at sbt.Execute.work(Execute.scala:244)
at sbt.Execute$$anonfun$submit$1.apply(Execute.scala:237)
at sbt.Execute$$anonfun$submit$1.apply(Execute.scala:237)
at sbt.ConcurrentRestrictions$$anon$4$$anonfun$1.apply(ConcurrentRestrictions.scala:160)
at sbt.CompletionService$$anon$2.call(CompletionService.scala:30)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
[error] (daffodil-lib/compile:genProps) Failed to generate code}}

It appears that clean is removing the gen-props jar, and then when trying to rebuild GeneratedCode.scala, sbt does not realize that it is deleted and needs to be rebuilt.