修改工程目录下的.project文件
普通工程下的该文件内容是：
<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
<name>xxx</name>
<comment></comment>
<projects>
</projects>
<buildSpec>
<buildCommand>
<name>org.eclipse.jdt.core.javabuilder</name>
<arguments>
</arguments>
</buildCommand>
</buildSpec>
<natures>
<nature>org.eclipse.jdt.core.javanature</nature>
</natures>
</projectDescription>

替换成下面
<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
<name>Pro</name>
<comment></comment>
<projects>
</projects>
<buildSpec>
<buildCommand>
<name>com.genuitec.eclipse.j2eedt.core.WebClasspathBuilder</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>org.eclipse.jdt.core.javabuilder</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>com.genuitec.eclipse.j2eedt.core.J2EEProjectValidator</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>com.genuitec.eclipse.j2eedt.core.DeploymentDescriptorValidator</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>org.eclipse.wst.validation.validationbuilder</name>
<arguments>
</arguments>
</buildCommand>
</buildSpec>
<natures>
<nature>com.genuitec.eclipse.j2eedt.core.webnature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
</natures>
</projectDescription>

另外在.class文件中设置：
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="src" path="src"/>
......
<classpathentry kind="output" path="WebRoot/WEB-INF/classes"/>
</classpath>

src和output中的path选择你对应的java工程路径名