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Or just use JIRA Command Line Interface addVersion which does the same thing.
SOAP or REST. Your program should establish a connection to Jira with one of those two, and talk to it that way.
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This API : http://confluence.atlassian.com/display/JIRA/API+Documentation ?
I found a "addVersion" in this API but I don't know if it's the best way.
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No, that's the Jira API - that relates to the internals of Jira and is for people who want to modify the core code in Jira, or more commonly, write plugins which are added to Jira and run within it.
You said you want a standalone program to run outside Jira, so you need the APIs that talk to Jira remotely. That's http://docs.atlassian.com/jira/REST/latest/ and http://confluence.atlassian.com/display/JIRADEV/Creating+a+SOAP+Client
As a general starting point, have a look at http://confluence.atlassian.com/display/JIRA/Appendix+A+-+Extending+JIRA
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