Bug 14421 Old .CLASS Files Are Not Deleted
When creating a project that does NOT use source folders (and does not use a bin directory for .class files) the .java and .class files are stored together in the Java package structure. When converting a project to use source folders (and the required bin directory for .class files), the old .class files stored in the Java package structure are NEVER DELETED by Eclipse. This is a bug for Eclipse 1.0 and 2.0. Since I use WSDD 4.0 (which is built on Eclipse 1.0), I've seen compilation errors due to the fact that the compiler/JDT is using old .class files rather than the new ones in the project's bin directory. I have not managed to reproduce the compile errors in build 20020416. But since the old .class files should have been deleted this is still a bug for the latest build.
org.eclipse.jdt.ui/ui/org/eclipse/jdt/ui/wizards/NewJavaProjectWizardPage.java
* The default output location will be applied when <code>initBuildPaths</code> is
	 * called. This is done automatically when the page becomes visible and
	 * the project or the default paths have changed.
	 * </p>
	 *
	 * @param entries the default classpath entries
	 * @param appendDefaultJRE <code>true</code> a variable entry for the
	 *  default JRE (specified in the preferences) will be added to the classpath.
	 */
	public void setDefaultClassPath(IClasspathEntry[] entries, boolean appendDefaultJRE) {
		if (entries != null && appendDefaultJRE) {
			IClasspathEntry[] newEntries= new IClasspathEntry[entries.length + 1];
			System.arraycopy(entries, 0, newEntries, 0, entries.length);
			newEntries[entries.length]= JavaRuntime.getJREVariableEntry();
			entries= newEntries;
		}
		fClasspathEntries= entries;
		fAddJRE= appendDefaultJRE;
		setProjectModified();
	}
	
	/**
	 * Sets the project to modified. This will initialize the page when becomes visible.
	 */
	public void setProjectModified() {
		fProjectModified= true;
	}
	/**
	 * Gets the project handle from the main page.
	 * Overwrite this method if you do not have a main page