Classifiers can also be specified at the command-line. See http://maven.apache.org/plugins/maven-install-plugin/install-file-mojo.html#classifier.
Javadoc and sources are just artifacts with a classifier of the same pom.
For example:
Install the main artifact
mvn install:install-file -Dfile=matlabcontrol-4.1.0.jar
-DgroupId=matlab -DartifactId=matlab -Dversion=4.1.0
Install the javadoc using the classifier javadoc:
mvn install:install-file -Dfile=matlabcontrol-4.1.0.jar
-DgroupId=matlab -DartifactId=matlab -Dversion=4.1.0 -Dclassifier=javadoc