[R] make all customizations to meet strict standard of cran

python-package/MANIFEST.in

@@ -1,14 +1,11 @@
-include *.sh *.md *.rst
+include *.md *.rst
 recursive-include xgboost *
-recursive-include xgboost/wrapper *
-recursive-include xgboost/windows *
-recursive-include xgboost/subtree *
+recursive-include xgboost/include *
 recursive-include xgboost/src *
-recursive-include xgboost/multi-node *
 #exclude pre-compiled .o file for less confusions
 #include the pre-compiled .so is needed as a placeholder
 #since it will be copy after compiling on the fly
-global-exclude xgboost/wrapper/*.so.gz
+global-exclude xgboost/build/*
 global-exclude xgboost/*.o
 global-exclude *.pyo
 global-exclude *.pyc