Notes: You need to root your phone first.
# restarts the adbd daemon with root permissions
# remounts the /system partition on the device read-write
# get the whitelist file from device
adb pull /system/etc/nfcee_access.xml
# export certificate to nfcee_access.xml
keytool -exportcert -v -keystore ~/.android/my-release-key.keystore -alias alias_name -storepass password|xxd -p -|tr -d '\n' >> nfcee_access.xml
# The cert is added to the end of the file. You must edit it to add proper tag.
# copy the whitelist file back to device
adb push nfcee_access.xml /system/etc/