1. Create JSF2 project (I guess it can be any dynamic web project)
2. Deploy it to AS6.M5 (haven't try on other servers)
3. Start the server
4. Remove any JAR from WEB-INF/lib folder
5. I get a lot of IOExceptions and the project is not built anymore
6. Stopping server/re-building project doesn't help. In debugger I see that all the threads which try to open any JAR in class path (at least from AS/common/lib folder) fail with ZipException
7. Only restarting Eclipse can help.

Here are the exceptions (a lot of them):

org.eclipse.core.runtime.CoreException: I/O exception
at org.eclipse.jdt.internal.core.JavaModelManager.getZipFile(JavaModelManager.java:2524)
at org.eclipse.jdt.internal.core.JarPackageFragmentRoot.getJar(JarPackageFragmentRoot.java:152)
at org.eclipse.jdt.internal.core.JarPackageFragmentRoot.computeChildren(JarPackageFragmentRoot.java:78)
at org.eclipse.jdt.internal.core.JavaProjectElementInfo.initializePackageNames(JavaProjectElementInfo.java:252)
at org.eclipse.jdt.internal.core.JavaProjectElementInfo.getProjectCache(JavaProjectElementInfo.java:225)
at org.eclipse.jdt.internal.core.JavaProjectElementInfo.newNameLookup(JavaProjectElementInfo.java:290)
at org.eclipse.jdt.internal.core.JavaProject.newNameLookup(JavaProject.java:2282)
at org.eclipse.jdt.internal.core.SearchableEnvironment.<init>(SearchableEnvironment.java:57)
at org.eclipse.jdt.internal.core.SearchableEnvironment.<init>(SearchableEnvironment.java:64)
at org.eclipse.jdt.internal.core.CancelableNameEnvironment.<init>(CancelableNameEnvironment.java:26)
at org.eclipse.jdt.internal.core.CompilationUnitProblemFinder.process(CompilationUnitProblemFinder.java:162)
at org.eclipse.jdt.internal.core.CompilationUnitProblemFinder.process(CompilationUnitProblemFinder.java:255)
at org.eclipse.jdt.internal.core.ReconcileWorkingCopyOperation.makeConsistent(ReconcileWorkingCopyOperation.java:190)
at org.eclipse.jdt.internal.core.ReconcileWorkingCopyOperation.executeOperation(ReconcileWorkingCopyOperation.java:89)
at org.eclipse.jdt.internal.core.JavaModelOperation.run(JavaModelOperation.java:728)
at org.eclipse.jdt.internal.core.JavaModelOperation.runOperation(JavaModelOperation.java:788)
at org.eclipse.jdt.internal.core.CompilationUnit.reconcile(CompilationUnit.java:1244)
at org.eclipse.jdt.internal.ui.text.java.JavaReconcilingStrategy.reconcile(JavaReconcilingStrategy.java:126)
at org.eclipse.jdt.internal.ui.text.java.JavaReconcilingStrategy.access$0(JavaReconcilingStrategy.java:108)
at org.eclipse.jdt.internal.ui.text.java.JavaReconcilingStrategy$1.run(JavaReconcilingStrategy.java:89)
at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
at org.eclipse.jdt.internal.ui.text.java.JavaReconcilingStrategy.reconcile(JavaReconcilingStrategy.java:87)
at org.eclipse.jdt.internal.ui.text.java.JavaReconcilingStrategy.initialReconcile(JavaReconcilingStrategy.java:178)
at org.eclipse.jdt.internal.ui.text.CompositeReconcilingStrategy.initialReconcile(CompositeReconcilingStrategy.java:114)
at org.eclipse.jdt.internal.ui.text.JavaCompositeReconcilingStrategy.initialReconcile(JavaCompositeReconcilingStrategy.java:133)
at org.eclipse.jface.text.reconciler.MonoReconciler.initialProcess(MonoReconciler.java:105)
at org.eclipse.jdt.internal.ui.text.JavaReconciler.initialProcess(JavaReconciler.java:398)
at org.eclipse.jface.text.reconciler.AbstractReconciler$BackgroundThread.run(AbstractReconciler.java:173)
Caused by: java.util.zip.ZipException: error in opening zip file
at java.util.zip.ZipFile.open(Native Method)
at java.util.zip.ZipFile.<init>(ZipFile.java:114)
at java.util.zip.ZipFile.<init>(ZipFile.java:131)
at org.eclipse.jdt.internal.core.JavaModelManager.getZipFile(JavaModelManager.java:2518)
... 27 more