No, the builder is not in the .project file. What does this builder do? What process should put it in there?
Many. Here are some of them. (Some of them were just file not found exceptions which appear to have been caused when I fiddled with a classpath setting while banging my head against a wall :p )
!ENTRY org.jboss.tools.common.model 2 0 2011-03-18 17:24:46.160
!MESSAGE Project P/gekko has corrupted nature: org.jboss.tools.jsf.jsfnature
!ENTRY org.jboss.tools.common.model 2 0 2011-03-18 17:25:03.094
!MESSAGE Project P/gekko has corrupted nature: org.jboss.tools.jsf.jsfnature
!ENTRY org.jboss.tools.common.model 2 0 2011-03-18 17:25:34.620
!MESSAGE Project P/gekko has corrupted nature: org.jboss.tools.jsf.jsfnature
!ENTRY org.eclipse.wst.common.project.facet.core 4 0 2011-03-18 17:28:04.137
!MESSAGE Project facet jbt.bpel.facet.core has not been defined. It is used in plugin org.jboss.ide.eclipse.as.core.
!ENTRY org.eclipse.wst.common.project.facet.core 4 0 2011-03-18 17:29:53.006
!MESSAGE Failed while installing Dynamic Web Module 2.5.
!STACK 0
java.lang.NullPointerException
at org.eclipse.jst.jee.model.internal.WebAnnotationReader.analyzeCompilationUnit(WebAnnotationReader.java:144)
at org.eclipse.jst.jee.model.internal.WebAnnotationReader.loadModel(WebAnnotationReader.java:99)
at org.eclipse.jst.jee.model.internal.common.AbstractAnnotationModelProvider.getConcreteModel(AbstractAnnotationModelProvider.java:106)
at org.eclipse.jst.jee.model.internal.common.AbstractAnnotationModelProvider.getModelObject(AbstractAnnotationModelProvider.java:122)
at org.eclipse.jst.jee.model.internal.common.AbstractMergedModelProvider.loadProviders(AbstractMergedModelProvider.java:265)
at org.eclipse.jst.jee.model.internal.common.AbstractMergedModelProvider.access$2(AbstractMergedModelProvider.java:255)
at org.eclipse.jst.jee.model.internal.common.AbstractMergedModelProvider$LoadModelsWorkspaceRunnable.run(AbstractMergedModelProvider.java:278)
at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:1975)
at org.eclipse.jst.jee.model.internal.common.AbstractMergedModelProvider.loadModel(AbstractMergedModelProvider.java:249)
at org.eclipse.jst.jee.model.internal.common.AbstractMergedModelProvider.getMergedModel(AbstractMergedModelProvider.java:219)
at org.eclipse.jst.jee.model.internal.Web25MergedModelProvider.modify(Web25MergedModelProvider.java:80)
at org.eclipse.jst.j2ee.web.project.facet.WebFacetInstallDelegate.populateDefaultContent(WebFacetInstallDelegate.java:283)
at org.eclipse.jst.j2ee.web.project.facet.WebFacetInstallDelegate.createWeb25DeploymentDescriptor(WebFacetInstallDelegate.java:246)
at org.eclipse.jst.j2ee.web.project.facet.WebFacetInstallDelegate.execute(WebFacetInstallDelegate.java:117)
at org.eclipse.wst.common.project.facet.core.internal.FacetedProject.callDelegate(FacetedProject.java:1478)
at org.eclipse.wst.common.project.facet.core.internal.FacetedProject.modifyInternal(FacetedProject.java:442)
at org.eclipse.wst.common.project.facet.core.internal.FacetedProject.mergeChangesInternal(FacetedProject.java:1182)
at org.eclipse.wst.common.project.facet.core.internal.FacetedProject.access$2(FacetedProject.java:1118)
at org.eclipse.wst.common.project.facet.core.internal.FacetedProject$1.run(FacetedProject.java:325)
at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:1975)
at org.eclipse.wst.common.project.facet.core.internal.FacetedProject.modify(FacetedProject.java:340)
at org.eclipse.wst.common.componentcore.internal.operation.FacetProjectCreationOperation.execute(FacetProjectCreationOperation.java:83)
at org.jboss.tools.jst.web.ui.operation.WebNatureOperation.createWTPNature2(WebNatureOperation.java:482)
at org.jboss.tools.jst.web.ui.operation.WebNatureOperation.run(WebNatureOperation.java:246)
at org.eclipse.ui.actions.WorkspaceModifyDelegatingOperation.execute(WorkspaceModifyDelegatingOperation.java:69)
at org.eclipse.ui.actions.WorkspaceModifyOperation$1.run(WorkspaceModifyOperation.java:106)
at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:1975)
at org.eclipse.ui.actions.WorkspaceModifyOperation.run(WorkspaceModifyOperation.java:118)
at org.eclipse.jface.operation.ModalContext.runInCurrentThread(ModalContext.java:464)
at org.eclipse.jface.operation.ModalContext.run(ModalContext.java:372)
at org.eclipse.jface.wizard.WizardDialog.run(WizardDialog.java:1008)
at org.jboss.tools.jst.web.ui.wizards.project.ImportWebProjectWizard.performFinish(ImportWebProjectWizard.java:91)
at org.eclipse.jface.wizard.WizardDialog.finishPressed(WizardDialog.java:811)
at org.eclipse.jface.wizard.WizardDialog.buttonPressed(WizardDialog.java:430)
at org.eclipse.jface.dialogs.Dialog$2.widgetSelected(Dialog.java:624)
at org.eclipse.swt.widgets.TypedListener.handleEvent(TypedListener.java:234)
at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1053)
at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:4066)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3657)
at org.eclipse.jface.window.Window.runEventLoop(Window.java:825)
at org.eclipse.jface.window.Window.open(Window.java:801)
at org.jboss.tools.common.model.ui.action.AddNatureActionDelegate.doRun(AddNatureActionDelegate.java:60)
at org.jboss.tools.common.model.ui.action.AddNatureActionDelegate.run(AddNatureActionDelegate.java:49)
at org.eclipse.ui.internal.PluginAction.runWithEvent(PluginAction.java:251)
at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:584)
at org.eclipse.jface.action.ActionContributionItem.access$2(ActionContributionItem.java:501)
at org.eclipse.jface.action.ActionContributionItem$5.handleEvent(ActionContributionItem.java:411)
at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1053)
at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:4066)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3657)
at org.eclipse.ui.internal.Workbench.runEventLoop(Workbench.java:2640)
at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:2604)
at org.eclipse.ui.internal.Workbench.access$4(Workbench.java:2438)
at org.eclipse.ui.internal.Workbench$7.run(Workbench.java:671)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:664)
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:149)
at org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:115)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:369)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:620)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:575)
at org.eclipse.equinox.launcher.Main.run(Main.java:1408)
!ENTRY org.jboss.tools.jst.web.ui 4 0 2011-03-18 17:29:53.006
!MESSAGE Failed while installing Dynamic Web Module 2.5.
!STACK 0
org.eclipse.core.commands.ExecutionException: Failed while installing Dynamic Web Module 2.5.
at org.eclipse.wst.common.componentcore.internal.operation.FacetProjectCreationOperation.execute(FacetProjectCreationOperation.java:110)
at org.jboss.tools.jst.web.ui.operation.WebNatureOperation.createWTPNature2(WebNatureOperation.java:482)
at org.jboss.tools.jst.web.ui.operation.WebNatureOperation.run(WebNatureOperation.java:246)
at org.eclipse.ui.actions.WorkspaceModifyDelegatingOperation.execute(WorkspaceModifyDelegatingOperation.java:69)
at org.eclipse.ui.actions.WorkspaceModifyOperation$1.run(WorkspaceModifyOperation.java:106)
at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:1975)
at org.eclipse.ui.actions.WorkspaceModifyOperation.run(WorkspaceModifyOperation.java:118)
at org.eclipse.jface.operation.ModalContext.runInCurrentThread(ModalContext.java:464)
at org.eclipse.jface.operation.ModalContext.run(ModalContext.java:372)
at org.eclipse.jface.wizard.WizardDialog.run(WizardDialog.java:1008)
at org.jboss.tools.jst.web.ui.wizards.project.ImportWebProjectWizard.performFinish(ImportWebProjectWizard.java:91)
at org.eclipse.jface.wizard.WizardDialog.finishPressed(WizardDialog.java:811)
at org.eclipse.jface.wizard.WizardDialog.buttonPressed(WizardDialog.java:430)
at org.eclipse.jface.dialogs.Dialog$2.widgetSelected(Dialog.java:624)
at org.eclipse.swt.widgets.TypedListener.handleEvent(TypedListener.java:234)
at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1053)
at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:4066)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3657)
at org.eclipse.jface.window.Window.runEventLoop(Window.java:825)
at org.eclipse.jface.window.Window.open(Window.java:801)
at org.jboss.tools.common.model.ui.action.AddNatureActionDelegate.doRun(AddNatureActionDelegate.java:60)
at org.jboss.tools.common.model.ui.action.AddNatureActionDelegate.run(AddNatureActionDelegate.java:49)
at org.eclipse.ui.internal.PluginAction.runWithEvent(PluginAction.java:251)
at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:584)
at org.eclipse.jface.action.ActionContributionItem.access$2(ActionContributionItem.java:501)
at org.eclipse.jface.action.ActionContributionItem$5.handleEvent(ActionContributionItem.java:411)
at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1053)
at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:4066)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3657)
at org.eclipse.ui.internal.Workbench.runEventLoop(Workbench.java:2640)
at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:2604)
at org.eclipse.ui.internal.Workbench.access$4(Workbench.java:2438)
at org.eclipse.ui.internal.Workbench$7.run(Workbench.java:671)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:664)
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:149)
at org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:115)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:369)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:620)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:575)
at org.eclipse.equinox.launcher.Main.run(Main.java:1408)
Caused by: org.eclipse.wst.common.project.facet.core.FacetedProjectFrameworkException: Failed while installing Dynamic Web Module 2.5.
at org.eclipse.wst.common.project.facet.core.internal.FacetedProject.callDelegate(FacetedProject.java:1508)
at org.eclipse.wst.common.project.facet.core.internal.FacetedProject.modifyInternal(FacetedProject.java:442)
at org.eclipse.wst.common.project.facet.core.internal.FacetedProject.mergeChangesInternal(FacetedProject.java:1182)
at org.eclipse.wst.common.project.facet.core.internal.FacetedProject.access$2(FacetedProject.java:1118)
at org.eclipse.wst.common.project.facet.core.internal.FacetedProject$1.run(FacetedProject.java:325)
at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:1975)
at org.eclipse.wst.common.project.facet.core.internal.FacetedProject.modify(FacetedProject.java:340)
at org.eclipse.wst.common.componentcore.internal.operation.FacetProjectCreationOperation.execute(FacetProjectCreationOperation.java:83)
... 50 more
Caused by: java.lang.NullPointerException
at org.eclipse.jst.jee.model.internal.WebAnnotationReader.analyzeCompilationUnit(WebAnnotationReader.java:144)
at org.eclipse.jst.jee.model.internal.WebAnnotationReader.loadModel(WebAnnotationReader.java:99)
at org.eclipse.jst.jee.model.internal.common.AbstractAnnotationModelProvider.getConcreteModel(AbstractAnnotationModelProvider.java:106)
at org.eclipse.jst.jee.model.internal.common.AbstractAnnotationModelProvider.getModelObject(AbstractAnnotationModelProvider.java:122)
at org.eclipse.jst.jee.model.internal.common.AbstractMergedModelProvider.loadProviders(AbstractMergedModelProvider.java:265)
at org.eclipse.jst.jee.model.internal.common.AbstractMergedModelProvider.access$2(AbstractMergedModelProvider.java:255)
at org.eclipse.jst.jee.model.internal.common.AbstractMergedModelProvider$LoadModelsWorkspaceRunnable.run(AbstractMergedModelProvider.java:278)
at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:1975)
at org.eclipse.jst.jee.model.internal.common.AbstractMergedModelProvider.loadModel(AbstractMergedModelProvider.java:249)
at org.eclipse.jst.jee.model.internal.common.AbstractMergedModelProvider.getMergedModel(AbstractMergedModelProvider.java:219)
at org.eclipse.jst.jee.model.internal.Web25MergedModelProvider.modify(Web25MergedModelProvider.java:80)
at org.eclipse.jst.j2ee.web.project.facet.WebFacetInstallDelegate.populateDefaultContent(WebFacetInstallDelegate.java:283)
at org.eclipse.jst.j2ee.web.project.facet.WebFacetInstallDelegate.createWeb25DeploymentDescriptor(WebFacetInstallDelegate.java:246)
at org.eclipse.jst.j2ee.web.project.facet.WebFacetInstallDelegate.execute(WebFacetInstallDelegate.java:117)
at org.eclipse.wst.common.project.facet.core.internal.FacetedProject.callDelegate(FacetedProject.java:1478)
... 57 more
!ENTRY org.jboss.tools.common.model 2 0 2011-03-18 17:33:37.572
!MESSAGE Project P/gekko has corrupted nature: org.jboss.tools.jsf.jsfnature
!ENTRY org.jboss.tools.common.model 2 0 2011-03-18 17:33:38.884
!MESSAGE Project P/gekko has corrupted nature: org.jboss.tools.jsf.jsfnature
I can't give a final answer to this question yet. Friday it appeared to be inconsistent at times. But after rebooting eclipse and a full clean rebuild of the project it seemed to stabalise. I'll keep an eye on this and let you know if I have problems.