If you add an input, Splunk adds that input to a copy of inputs.conf that belongs to the app you're in when you add that input. This means that if you navigated to Splunk Manager, directly from the Launcher your input will be added to $SPLUNK_HOME/etc/apps/launcher/local/inputs.conf.
http://docs.splunk.com/Documentation/Splunk/latest/User/AddDataToYourIndexes
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