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/expected_output/output.txt

@@ -0,0 +1,20 @@
+SourceFilePath: "my-app/src/main/java/com/mycompany/app/Bar.java"
+	LanguageStandard: "10"
+	ClassPathItem: "test/jre/system/library/path.jar"
+	ClassPathItem: "my-app/src/main/java"
+	ClassPathItem: "my-app/src/test/java"
+SourceFilePath: "my-app/src/main/java/com/mycompany/app/FooBar.java"
+	LanguageStandard: "10"
+	ClassPathItem: "test/jre/system/library/path.jar"
+	ClassPathItem: "my-app/src/main/java"
+	ClassPathItem: "my-app/src/test/java"
+SourceFilePath: "my-app/src/main/java/com/mycompany/app/Main.java"
+	LanguageStandard: "10"
+	ClassPathItem: "test/jre/system/library/path.jar"
+	ClassPathItem: "my-app/src/main/java"
+	ClassPathItem: "my-app/src/test/java"
+SourceFilePath: "my-app/src/test/java/com/mycompany/app/AppTest.java"
+	LanguageStandard: "10"
+	ClassPathItem: "test/jre/system/library/path.jar"
+	ClassPathItem: "my-app/src/main/java"
+	ClassPathItem: "my-app/src/test/java"

bin/test/data/SourceGroupTestSuite/java_maven/input/my-app/pom.xml

@@ -0,0 +1,18 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>com.mycompany.app</groupId>
+  <artifactId>my-app</artifactId>
+  <packaging>jar</packaging>
+  <version>1.0-SNAPSHOT</version>
+  <name>my-app</name>
+  <url>http://maven.apache.org</url>
+  <dependencies>
+    <dependency>
+      <groupId>junit</groupId>
+      <artifactId>junit</artifactId>
+      <version>3.8.1</version>
+      <scope>test</scope>
+    </dependency>
+  </dependencies>
+</project>

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 );
+    }
+}