Fix bug on freevar

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala

@@ -21,9 +21,9 @@ import nl.lumc.sasc.biopet.utils.ConfigUtils.ImplicitConversions
 
 trait Configurable extends ImplicitConversions {
   val root: Configurable
-  def configPath: List[String] = if (root != null) root.configFullPath else List()
-  protected lazy val configName = getClass.getSimpleName.toLowerCase
-  protected lazy val configFullPath = configName :: configPath
+  lazy val configPath: List[String] = if (root != null) root.configFullPath else List()
+  protected[config] lazy val configName = getClass.getSimpleName.toLowerCase
+  protected[config] lazy val configFullPath: List[String] = configPath ::: configName :: Nil
   var defaults: scala.collection.mutable.Map[String, Any] = if (root != null) scala.collection.mutable.Map(root.defaults.toArray: _*)
   else scala.collection.mutable.Map()
 
@@ -32,7 +32,7 @@ trait Configurable extends ImplicitConversions {
   protected class ConfigFunctions {
     def apply(key: String, default: Any = null, submodule: String = null, required: Boolean = false, freeVar: Boolean = true): ConfigValue = {
       val m = if (submodule != null) submodule else configName
-      val p = (if (submodule != null) configName :: configPath else configPath).reverse
+      val p = (if (submodule != null) configName :: configPath else configPath)
       val d = {
         val value = Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar))
         if (value.isDefined) value.get.value else default
@@ -43,13 +43,13 @@ trait Configurable extends ImplicitConversions {
           throw new IllegalStateException("Value in config could not be found but it is required, key: " + key + "   module: " + m + "   path: " + p)
         } else return null
       }
-      if (d == null) return Config.global(m, p, key, freeVar)
+      if (d == null) return Config.global(m, p, key, freeVar = freeVar)
       else return Config.global(m, p, key, d, freeVar)
     }
 
     def contains(key: String, submodule: String = null, freeVar: Boolean = true) = {
       val m = if (submodule != null) submodule else configName
-      val p = (if (submodule != null) configName :: configPath else configPath).reverse
+      val p = (if (submodule != null) configName :: configPath else configPath)
 
       Config.global.contains(m, p, key, freeVar) || !(Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar)) == None)
     }