Correctly handle directories in Slicer

Fixes #44

sdg-cli/src/main/java/es/upv/mist/slicing/cli/Slicer.java

@@ -22,6 +22,7 @@ import java.io.PrintWriter;
 import java.util.*;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
+import java.util.stream.Stream;
 
 public class Slicer {
     protected static final String HELP_HEADER = "Java SDG Slicer: extract a slice from a Java program. At least" +
@@ -217,8 +218,13 @@ public class Slicer {
         // Build the SDG
         NodeList<CompilationUnit> units = new NodeList<>();
         try {
-            for (File directory : dirIncludeSet)
-                units.add(StaticJavaParser.parse(directory));
+            for (File file : dirIncludeSet) {
+                if (file.isDirectory())
+                    for (File f : (Iterable<File>) findAllJavaFiles(file)::iterator)
+                        units.add(StaticJavaParser.parse(f));
+                else
+                    units.add(StaticJavaParser.parse(file));
+            }
             CompilationUnit scUnit = StaticJavaParser.parse(scFile);
             if (!units.contains(scUnit))
                 units.add(scUnit);
@@ -258,6 +264,24 @@ public class Slicer {
         }
     }
 
+    protected Stream<File> findAllJavaFiles(File directory) {
+        Stream.Builder<File> builder = Stream.builder();
+        findAllJavaFiles(directory, builder);
+        return builder.build();
+    }
+
+    protected void findAllJavaFiles(File directory, Stream.Builder<File> builder) {
+        File[] files = directory.listFiles();
+        if (files == null)
+            return;
+        for (File f : files) {
+            if (f.isDirectory())
+                findAllJavaFiles(f, builder);
+            else if (f.getName().endsWith(".java"))
+                builder.add(f);
+        }
+    }
+
     protected String getDisclaimer(CompilationUnit.Storage s) {
         return String.format("\n\tThis file was automatically generated as part of a slice with criterion" +
                         "\n\tfile: %s, line: %d, variable(s): %s\n\tOriginal file: %s\n",