updates on files, removed obsolete file

Makefile

@@ -10,7 +10,9 @@ clean:
 	@rm -rf bin
 	@rm -rf build
 	@rm -rf debug
-	@rm -rf doc/html
-	@rm -rf doc/latex
-	@rm -rf gmon.out
 	@rm -rf cmake-build-debug
+	@rm -rf auto
+	@rm -rf doc/*/
+	@rm -rf _minted*
+	@rm -rf output.*
+	@rm -rf *.tex *.out