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DrJava has a very useful indenting algorithm, but indenting several large files can be a time consuming process. Because of this, DrJava provides a command line interface to its indenter that can be run on a series of files.
Use the following command at a command prompt to run the indenter on a series of files.
java -classpath drjava-DATE-TIME.jar edu.rice.cs.drjava.IndentFiles [-indent N] [filename.java...]
Replace DATE-TIME with the appropriate value for your DrJava file. The "-indent" argument is optional, where N is the number of spaces to use for an indentation level.