HADOOP-11464 reinstated support for running the bash scripts through Cygwin. The logic involves setting a cygwin flag variable to indicate if the script is executing through Cygwin. The flag is set in all of the interactive scripts: hadoop, hdfs, yarn and mapred. The flag is not set through hadoop-daemon.sh though. This can cause an erroneous overwrite of HADOOP_HOME and JAVA_LIBRARY_PATH inside hadoop-config.sh.