<extension
    id="examplenature"
    name="Example nature"
    point="org.eclipse.core.resources.natures">
    <runtime>
        <run
            class="com.example.product.ExampleProjectNature">
        </run>
    </runtime>
    <requires-nature
            id="org.eclipse.jdt.core.javanature">
    </requires-nature>
</extension>

IProject project = // get project...
IProjectDescription description = project.getDescription();

String[] natures = description.getNatureIds();
String[] newNatures = new String[natures.length + 1];
System.arraycopy(natures, 0, newNatures, 0, natures.length);
newNatures[natures.length] = ExampleProjectNature.NATURE_ID;

// validate the natures
IWorkspace workspace = ResourcesPlugin.getWorkspace();
IStatus status = workspace.validateNatureSet(newNatures);

// only apply new nature, if the status is ok
if (status.getCode() == IStatus.OK) {
    description.setNatureIds(newNatures);
    project.setDescription(description, null);
}

<extension
    point="org.eclipse.core.expressions.definitions">
    <definition
        id="com.example.project.hasNature">
        <adapt
            type="org.eclipse.core.resources.IProject">
            <test
                property="org.eclipse.core.resources.projectNature"
                value="com.example.project.examplenature">
            </test>
        </adapt>
    </definition>
</extension>

import org.eclipse.core.resources.IProject;
import org.eclipse.core.resources.IProjectNature;
import org.eclipse.core.runtime.CoreException;

public class ExampleProjectNature implements IProjectNature {

    // ID of the natures, which consists of Bundle-SymbolicName + ID
    public static final String NATURE_ID = "com.example.project.examplenature";

    private IProject project;

    @Override
    public void configure() throws CoreException {
        // only called once the nature has been set
        
        // configure the project...
    }

    @Override
    public void deconfigure() throws CoreException {
        // only called once the nature has been set     
        
        // reset the project configuration...
    }

    @Override
    public IProject getProject() {
        return project;
    }

    @Override
    public void setProject(IProject project) {
        this.project = project;
    }

}

import org.eclipse.core.commands.AbstractHandler;
import org.eclipse.core.commands.ExecutionEvent;
import org.eclipse.core.commands.ExecutionException;
import org.eclipse.core.commands.IHandler;
import org.eclipse.core.resources.IProject;
import org.eclipse.core.resources.IProjectDescription;
import org.eclipse.core.resources.IResource;
import org.eclipse.core.resources.IWorkspace;
import org.eclipse.core.resources.ResourcesPlugin;
import org.eclipse.core.runtime.CoreException;
import org.eclipse.core.runtime.IAdapterManager;
import org.eclipse.core.runtime.IStatus;
import org.eclipse.core.runtime.Platform;
import org.eclipse.jface.viewers.ISelection;
import org.eclipse.jface.viewers.IStructuredSelection;
import org.eclipse.ui.handlers.HandlerUtil;

import com.example.product.ExampleProductNature;

public class ExampleProjectNatureHandler extends AbstractHandler {

    @Override
    public Object execute(ExecutionEvent event) throws ExecutionException {

        ISelection currentSelection = HandlerUtil.getCurrentSelection(event);
        if (currentSelection instanceof IStructuredSelection) {

            Object firstElement = ((IStructuredSelection) currentSelection).getFirstElement();
            
            // Get an IResource as an adapter from the current selection
            IAdapterManager adapterManager = Platform.getAdapterManager();
            IResource resourceAdapter = adapterManager.getAdapter(firstElement, IResource.class);
            
            if (resourceAdapter != null) {
                IResource resource = resourceAdapter;
                IProject project = resource.getProject();
                try {
                    IProjectDescription description = project.getDescription();
                    String[] natures = description.getNatureIds();
                    String[] newNatures = new String[natures.length + 1];
                    System.arraycopy(natures, 0, newNatures, 0, natures.length);
                    
                    // add our new "com.example.project.examplenature" id
                    newNatures[natures.length] = ExampleProjectNature.NATURE_ID;

                    // validate the natures
                    IWorkspace workspace = ResourcesPlugin.getWorkspace();
                    IStatus status = workspace.validateNatureSet(newNatures);

                    // only apply new nature, if the status is ok
                    if (status.getCode() == IStatus.OK) {
                        description.setNatureIds(newNatures);
                        project.setDescription(description, null);
                    }
                    
                    return status;
                } catch (CoreException e) {
                    throw new ExecutionException(e.getMessage(), e);
                }
            }
        }

        return Status.OK_STATUS;
    }

}

import org.eclipse.swt.SWT;
import org.eclipse.swt.widgets.Composite;
import org.eclipse.swt.widgets.Control;
import org.eclipse.swt.widgets.Label;
import org.eclipse.ui.IWorkbenchPropertyPage;
import org.eclipse.ui.dialogs.PropertyPage;

public class ExamplePropertyPage extends PropertyPage implements IWorkbenchPropertyPage {

    @Override
    protected Control createContents(Composite parent) {
        
        // There will be no default, therefore remove default button
        noDefaultButton();
        
        Label label = new Label(parent, SWT.NONE);
        label.setText("PropertyPage example.");
        
        return label;
    }

}