O seguinte funciona para desinstalar
wget http://cygwin.org/setup-x86_64.exe
chmod 766 setup-x86_64.exe
./setup-x86_64.exe -nq -x wget
e o seguinte funciona para instalar pacotes
./setup-x86_64.exe -nq -P autoconf,automake,binutils,cygport,cygwin-devel,gcc-core,git,libcom_err-devel,libcom_err2,libcrypt-devel,libcrypt0,libedit-devel,libedit0,libgcc1,libgssapi_krb5_2,libiconv-devel,libiconv2,libintl-devel,libintl8,libk5crypto3,libkrb5-devel,libkrb5_3,libkrb5support0,libncurses-devel,libncursesw10,libopenssl100,libssp0-4.9.2-3,make,openssl-devel,w32api-headers,w32api-includes,zlib-devel,zlib0-1.2.8-3,git,wget
e para ver todos os pacotes já instalados serem executados
cygcheck -c