The normal Java classloaders look for classes first in the bootstrap classpath, before checking for extensions and the application classpath. By default, the bootstrap classpath consists of the "rt.jar" file and some other important JAR files that are supplied by the JRE installation. These provide all of the classes in the standard Java SE class library, along with various "internal" implementation classes.
Under normal circumstances, you don't need to concern yourself with this. By default, commands like
javac and so on will use the appropriate versions of the runtime libraries.
Very occasionally, it is necessary to override the normal behavior of the Java runtime by using an alternative version of a class in the standard libraries. For example, you might encounter a "show stopper" bug in the runtime libraries that you cannot work around by normal means. In such a situation, it is possible to create a JAR file containing the altered class and then add it to the bootstrap classpath which launching the JVM.
java command provides the following
-X options for modifying the bootstrap classpath:
-Xbootclasspath:<path>replaces the current boot classpath with the path provided.
-Xbootclasspath/a:<path>appends the provided path to the current boot classpath.
-Xbootclasspath/p:<path>prepends the provided path to the current boot classpath.
Note that when use the bootclasspath options to replace or override a Java class (etcetera), you are technically modifying Java. There may be licensing implications if you then distribute your code. (Refer to the terms and conditions of the Java Binary License ... and consult a lawyer.)