Fixed --keep-prefix functionality.

Changing to keep include prefixes had two side effects: the main
file being parsed wasn't filtered out anymore, and include directory
paths would be added to the path in the include statement.

Also moved the include_test*.fbs files to sub directories so we
can actually test the handling of -I etc.

tested: on Linux.

Change-Id: Ibae095cea7ab0cccbac15cfb5171719f6b5cad8c

include/flatbuffers/idl.h

@@ -590,7 +590,8 @@ private:
   FLATBUFFERS_CHECKED_ERROR SkipJsonString();
   FLATBUFFERS_CHECKED_ERROR DoParse(const char *_source,
                                     const char **include_paths,
-                                    const char *source_filename);
+                                    const char *source_filename,
+                                    const char *include_filename);
   FLATBUFFERS_CHECKED_ERROR CheckClash(std::vector<FieldDef*> &fields,
                                        StructDef *struct_def,
                                        const char *suffix,