I am trying to run a java project that includes two libraries
classpathentry kind="lib" path="lib/jpbc-api-1.2.1.jar" sourcepath="lib/jpbc-api-1.2.1.jar"
classpathentry kind="lib" path="lib/jpbc-plaf-1.2.1.jar" sourcepath="jpbc-plaf-1.2.1.jar"
error: cannot find symbol
You don't need the compiler to run the program if it's already compiled by Eclipse - you only need the Java runtime. The .classpath file is Eclipse-specific, so it won't be used by either the Java compiler (javac) or the Java runtime (java).
Assuming that your main class is called com.my.MainClass and your classes directory is called "myclasses", you would run your class using this command line:
java -classpath lib/jpbc-api-1.2.1.jar;lib/jpbc-plaf-1.2.1.jar;myclasses com.my.MainClass
I think you should have a look at the documentation of the Java command line tools: http://docs.oracle.com/javase/7/docs/technotes/tools/windows/java.html http://docs.oracle.com/javase/7/docs/technotes/tools/windows/javac.html