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_maven/input/my-app/src/main/java/com/mycompany/app/Bar.java

@@ -0,0 +1,5 @@
+package com.mycompany.app;
+
+class Bar implements FooBar
+{
+}

bin/test/data/SourceGroupTestSuite/java_maven/input/my-app/src/main/java/com/mycompany/app/Foo.java

@@ -0,0 +1,5 @@
+package com.mycompany.app;
+
+class Foo implements FooBar
+{
+}

bin/test/data/SourceGroupTestSuite/java_maven/input/my-app/src/main/java/com/mycompany/app/FooBar.java

@@ -0,0 +1,5 @@
+package com.mycompany.app;
+
+public interface FooBar
+{
+}

bin/test/data/SourceGroupTestSuite/java_maven/input/my-app/src/main/java/com/mycompany/app/Main.java

@@ -0,0 +1,13 @@
+package com.mycompany.app;
+
+public class Main
+{
+	public Foo m_foo;
+	public Bar m_bar;
+	
+	public static void main( String[] args )
+    {
+        System.out.println( "Hello World!" );
+    }
+}
+

bin/test/data/SourceGroupTestSuite/java_maven/input/my-app/src/test/java/com/mycompany/app/AppTest.java

@@ -0,0 +1,38 @@
+package com.mycompany.app;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+/**
+ * Unit test for simple App.
+ */
+public class AppTest 
+    extends TestCase
+{
+    /**
+     * Create the test case
+     *
+     * @param testName name of the test case
+     */
+    public AppTest( String testName )
+    {
+        super( testName );
+    }
+
+    /**
+     * @return the suite of tests being tested
+     */
+    public static Test suite()
+    {
+        return new TestSuite( AppTest.class );
+    }
+
+    /**
+     * Rigourous Test :-)
+     */
+    public void testApp()
+    {
+        assertTrue( true );
+    }
+}