logic: indexer command refactoring

* moved SystemHeaderSearchPaths and FramewordSeearchPaths of indexer cxx indexer commands to CompilerFlags section
* added SourceGroupTestSuite to test indexer command generation of all source groups
* removed "compile_commands.json" from gitignore, because a resource file for the tests has this name

bin/test/data/SourceGroupTestSuite/java_gradle/input/src/main/java/hello/Greeter.java

@@ -0,0 +1,7 @@
+package hello;
+
+public class Greeter {
+  public String sayHello() {
+    return "Hello world!";
+  }
+}

bin/test/data/SourceGroupTestSuite/java_gradle/input/src/main/java/hello/HelloWorld.java

@@ -0,0 +1,13 @@
+package hello;
+
+import org.joda.time.LocalTime;
+
+public class HelloWorld {
+  public static void main(String[] args) {
+    LocalTime currentTime = new LocalTime();
+    System.out.println("The current local time is: " + currentTime);
+
+    Greeter greeter = new Greeter();
+    System.out.println(greeter.sayHello());
+  }
+}

bin/test/data/SourceGroupTestSuite/java_gradle/input/src/test/java/hello/HelloWorldTests.java

@@ -0,0 +1,40 @@
+package hello;
+
+import java.io.ByteArrayOutputStream;
+import java.io.PrintStream;
+import java.nio.charset.StandardCharsets;
+
+import org.junit.Before;
+import org.junit.Test;
+
+import static org.hamcrest.CoreMatchers.containsString;
+import static org.junit.Assert.assertThat;
+
+public class HelloWorldTests {
+
+    private ByteArrayOutputStream baos = new ByteArrayOutputStream();
+    private PrintStream ps = new PrintStream(baos);
+
+    @Before
+    public void setup() {
+        System.setOut(ps);
+    }
+
+    @Test
+    public void shouldPrintTimeToConsole() {
+        HelloWorld.main(new String[] { });
+
+        assertThat(output(), containsString("The current local time is"));
+    }
+
+    @Test
+    public void shouldPrintHelloWorldToConsole() {
+        HelloWorld.main(new String[] { });
+
+        assertThat(output(), containsString("Hello world!"));
+    }
+
+    private String output() {
+        return new String(baos.toByteArray(), StandardCharsets.UTF_8);
+    }
+}