StandardValueSet should be used in the package.xml to retrieve and deploy Opportunity Stage picklist changes using Apache ANT Tool.

Sample package.xml:

<?xml version="1.0" encoding="UTF-8"?>  
<Package xmlns="http://soap.sforce.com/2006/04/metadata">    
    <types>  
        <members>OpportunityStage</members>  
        <name>StandardValueSet</name>  
    </types>        
    <version>43.0</version>        
</Package>