Project folder or project sub-folder right button menu option Rebuild folder will issue a javac command or compile command for all the files in the selected folder only.
Compile *.java folder command from the right button menu of the folder will issue "javac *.java" command in the directory of the top most Java file in the folder. This is useful when issuing javac command in various directories for a project. For example, if the top most Java file in the selected folder is in the directory c:\test then the command "javac *.java" will be issued in the directory c:\test even though the project directory may be different from c:\test.