Make Cipher Tool to work in non-Carbon environments

Implementing https://wso2.org/jira/browse/CARBON-15094
There is no "<PRODUCT_HOME>/conf" folder in wso2 server packs. Need to have a check if it is for wso2 product then the location should be "<PRODUCT_HOME>/repository/conf/security/". It is better to have it here since the SecureVault will look for the cipher-text.properties and secret-conf.properties.