Hey Senthil,
Is the app config file generated by your app? If so, you don't have to include it in the wyBuild project at all -- just let your app generate it automatically if it's missing (i.e. first run).
If your app doesn't generate missing config files, then simply include an example config file (e.g. "app config-example") that your app makes a copy of if the actual config file location if it's missing.