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/build.gradle

@@ -0,0 +1,31 @@
+apply plugin: 'java'
+apply plugin: 'eclipse'
+apply plugin: 'application'
+
+mainClassName = 'hello.HelloWorld'
+
+// tag::repositories[]
+repositories { 
+    mavenCentral() 
+}
+// end::repositories[]
+
+// tag::jar[]
+jar {
+    baseName = 'gs-gradle'
+    version =  '0.1.0'
+}
+// end::jar[]
+
+// tag::dependencies[]
+sourceCompatibility = 1.8
+targetCompatibility = 1.8
+
+dependencies {
+    compile "joda-time:joda-time:2.2"
+    testCompile "junit:junit:4.12"
+}
+// end::dependencies[]
+
+// tag::wrapper[]
+// end::wrapper[]