Fix FileRepository implementation for scripted

I was seeing spurious travis failures and I finally tracked it down to
the fact that in some cases, the project metabuild would sometimes use a
caching file tree repository instead of a polling repository. This
caused problems because the caching repository can take a few milliseconds
to detect changes in a directory. Because scripted copies the project
sources to the temporary test directory, it was possible for the project
meta build compilation to be initiated before the cache was aware of all
of the files.

The reason this happened was because scripted would create a state where
the remaining commands looked like:
List(sbtPopOnFailure, resumeFromFailure, notifyUsersAboutShell, iflast shell, ~compile, < 41684)
The ~compile command was causing the continuous flag to get set to true
which caused the default file tree repository task to return the caching
version. The reason for the continuous flag was so that when sbt is
started in a non-interactive mode where the command is to be repeated,
then we use the caching file tree repository. To support this use case,
we just need to check that the last command begins with `~`, not that
_any_ command begins with `~`.

main/src/main/scala/sbt/internal/FileManagement.scala

@@ -26,7 +26,7 @@ private[sbt] object FileManagement {
     val interactive = remaining.contains("shell") || remaining.lastOption.contains("iflast shell")
     val scripted = remaining.contains("setUpScripted")
 
-    val continuous = remaining.exists(_.startsWith(ContinuousExecutePrefix))
+    val continuous = remaining.lastOption.exists(_.startsWith(ContinuousExecutePrefix))
     if (!scripted && (interactive || continuous)) {
       FileTreeViewConfig
         .default(watchAntiEntropy.value, pollInterval.value, pollingDirectories.value)