If you want to connect to a Nuxeo repository from a third party java application, Nuxeo provides you the tools to generate your connector.
The recommended way to do remote connections is through HttpAutomationClient, please check that documentation for details.
The old, deprecated way is to use NuxeoClient, for which you can find examples at http://hg.nuxeo.org/addons/nuxeo-samples/file/1.6. Note that NuxeoClient requires EJB RMI to function, which is not usable with Tomcat for instance.
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