Keystore file exists but is empty?
I had exectly the same problem. Issue appear when you give path to keystore file without the file name. You have to give keystore file name with the path after -keystore option. This means in your case:
keytool -exportcert -alias freenthrowkey -keystore C:\Users\User\Documents\FreeNthrowkey\KEYSTOREFILENAME.jks
Using following commands should give you proper output:
keytool -list -keystore .keystore
If you are looking for a specific alias, you can also specify it in the command:
keytool -list -keystore .keystore -alias foo
Also, to generate signed APK I suggest you to use Android studio itself. Choose "Generate Signed APK" from Build menu of Android studio and follow the steps. It will generate proper keystore
at given path.