The plugins directory is by default below the ImageJ directory hierarchy, but it can be changed.
The “plugins.dir” property specifies the location of the parent of the plugins directory.
This property can be set from either the command line or from within a Java program that starts ImageJ.
For example, if you run ImageJ with the command:
java -Dplugins.dir=/Users/wayne -cp ij.jar ij.ImageJ
it will look for the plugins folder in the /Users/wayne/ directory.
This property can also be set in a program that launches ImageJ:
System.getProperties().setProperty("plugins.dir", "/users/wayne");\\ new ImageJ(null);