Add note to docs that the --list argument requires full command-line

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java

@@ -161,6 +161,9 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
     @Argument(fullName="useAllAnnotations", shortName="all", doc="Use all possible annotations (not for the faint of heart)", required=false)
     protected Boolean USE_ALL_ANNOTATIONS = false;
 
+    /**
+     * Note that the --list argument requires a fully resolved and correct command-line to work.
+     */
     @Argument(fullName="list", shortName="ls", doc="List the available annotations and exit")
     protected Boolean LIST = false;
 

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java

@@ -81,7 +81,7 @@ public class RecalibrationArgumentCollection {
     public File RECAL_CSV_FILE = null;
 
     /**
-     * List all implemented covariates.
+     * Note that the --list argument requires a fully resolved and correct command-line to work.
      */
     @Argument(fullName = "list", shortName = "ls", doc = "List the available covariates and exit", required = false)
     public boolean LIST_ONLY = false;

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java

@@ -126,7 +126,9 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
     @Input(fullName="goldStandard", shortName = "gold", doc="Evaluations that count calls at sites of true variation (e.g., indel calls) will use this argument as their gold standard for comparison", required=false)
     public RodBinding<VariantContext> goldStandard = null;
 
-    // Help arguments
+    /**
+     * Note that the --list argument requires a fully resolved and correct command-line to work.
+     */
     @Argument(fullName="list", shortName="ls", doc="List the available eval modules and exit", required=false)
     protected Boolean LIST = false;