As far i can understand you have a web project but structure different to dynamic web project. So you can add web project nature to the project using following-
IFacetedProject facetedProject = ProjectFacetsManager.create(project, true, null);
IFacetedProjectWorkingCopy workingCopy = facetedProject.createWorkingCopy();
IProjectFacet webFacet = ProjectFacetsManager.getProjectFacet("jst.web");
IProjectFacetVersion defaultWebFacet = webFacet.getDefaultVersion();
workingCopy.addProjectFacet(defaultWebFacet);
And then change the deployment settings using project ->properties->Deployment Assembly to map project resources that will go into WAR file. You can also configure this programatically using following code-
IVirtualComponent rootComponent = ComponentCore
.createComponent(project);
IFolder buildXwtFolder =//Source Folder;
IVirtualFolder rootFolder = rootComponent.getRootFolder();
IVirtualFolder subFolder = rootFolder.getFolder("Deploy path");
subFolder.createLink(buildXwtFolder.getProjectRelativePath(), 0,
null);
if (subFolder instanceof ITaggedVirtualResource) {
((ITaggedVirtualResource) subFolder).tagResource(
buildXwtFolder.getProjectRelativePath(),
null, null);
}