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I have Maven javadoc plugin working nicely right now, but I do not know how to add it to the remote directory via scp.
How do I transfer the javadoc files via scp, but AFTER they have been generated? Can this automatically happen when I call site:site?
Thanks!

maven-javadoc-plugin doesn't attach to any phase/goal by default, you need configure it manually in pom.xml.
See Generate Javadocs As Part Of Project Reports:
To generate javadocs as part of the site generation, you should add the Javadoc Plugin in the section of your pom:
<project>
...
<reporting>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.8.1</version>
<configuration>
...
</configuration>
</plugin>
</plugins>
...
</reporting>
...
</project>
When you execute mvn site, the javadocs will be generated and included in the generated site. A link to the javadocs will be added in the Project Reports menu.
Alternatively, if you use maven-release-plugin, javadoc generation (and upload) is automatically handled by default, see here:
The following delvierables are created and deployed to local and remoted repositories after the execution of the release:perform goal has finished.
artifact id-version.jar
The binaries for the current release of the project.
artifact id-version-javadoc.jar
The javadoc explaining the current functionality of the classes within the current release.
artifact id-version-source.jar
The source code revisions used to build the current release of the project.
artifact id-version.pom
The contents of the pom.xml file used to create the current release of the project.
If you want to attach javadoc generation to some phase/goal other than site, check out How to deploy Javadoc jar file?