Hello, Ralf.

My Analysis showing why Team Advisor pops up with a PermissionDeniedException regardless I catch the exception:

1) my code tries to get a workspace connection (context) in order to get the full path of all changed files in a changeset: wsManager.getWorkspaceConnection(...)
2) com.ibm.team.scm.client.internal.WorkspaceManager.getWorkspaceConnection(...) calls getServerConfigurationService().refreshWorkspaces(...)
3)  getServerConfigurationService().refreshWorkspaces(...) calls com.ibm.team.scm.client.internal.ScmServiceInterfaceProxy.invoke(...)
4) ScmServiceInterfaceProxy.invoke(...) calls ScmServiceInterfaceProxy.invokeCancelableService(...);
4.1. ScmServiceInterfaceProxy.invokeCancelableService(...) throws a PermissionDeniedException
4.2. ScmServiceInterfaceProxy.invoke(...) catches the exception
4.2.1. shows Team Advisor view using the notifyProcess(...) (see Step 4 in the code below)
4.2.2. and finally passes the exception to the caller IWorkspaceConnection getWorkspaceConnection(...) (see Step 5 in the code below)
5) IWorkspaceConnection getWorkspaceConnection(...) passes the exception to my code which is processed as well.  (see Step 7 in the code below)
 


My plug-in code:
    ....
    try {
        if(wsHandle != null) {

           // Step 1:  IWorkspaceConnection getWorkspaceConnection(...) is executed

            IWorkspaceConnection wsConn =
                wsManager.getWorkspaceConnection(
                     (IWorkspaceHandle) wsHandle,
                    child.newChild(25));
             ...
        }//if
        ...
    }//try
    catch(Throwable e) {
        // Step 7: The exception PermissionDeniedException is processed here as well
        System.out.println("Throwable: " + e.getMessage());
        return result;
    }

================================================
class: com.ibm.team.scm.client.internal.WorkspaceManager

public IWorkspaceConnection getWorkspaceConnection(
            IWorkspaceHandle workspace,
            IProgressMonitor monitor) throws TeamRepositoryException {
                                                  // Step 6: The exception is passed to the caller - my plug-in code
        ...

       if (conn == null) {

            // Step 2: getServerConfigurationService().refreshWorkspaces(...) is executed.
            //             It calls ScmServiceInterfaceProxy. invoke(...)
           WorkspaceRefreshResult refreshed = getServerConfigurationService().refreshWorkspaces(
                   new WorkspaceRefreshParameter[]{createEmptyWorkspaceRefreshParameter(workspace)},
                   SCMClientUtil.monitorFor(monitor))[0];
           ...
}

========================================================
//Proxy helper which wraps all RPC service interface objects to common progress monitoring and
  cancellation support
class: com.ibm.team.scm.client.internal.ScmServiceInterfaceProxy

 public Object invoke(Object proxy, final Method method, final Object[] args)
            throws Throwable {
    try {
           ...

            // Step 3: ScmServiceInterfaceProxy.invokeCancelableService(...) is executed.
           //              it throws PermissionDeniedException which is processed in ScmServiceInterfaceProxy. invoke(...)

            returnVal = invokeCancelableService(method, args, monitor);
            ...
    } catch (Throwable e) {
            TeamRepositoryException tre = null;
            ...
             tre = (TeamRepositoryException)e;
             ...
            if (tre != null) {

                     // Step 4: The exception is caught and Team Advisor is shown here
                     //             with the error message: Team Advisor Problem: Permission denied during
                     //             "Source Control Operation". User '...' does not have permission to read workspace '...'

                    // The exception is still thrown so that clients can
                   // clean-up and react accordingly.
                   if(!calledByTeamAdvisorView &&
                        (tre instanceof TeamOperationCanceledException
                       || tre instanceof PermissionDeniedException)) {                    
                           notifyProcess(tre, method); // shows TeamAdvisor view informing PermissionDeniedException error
                    }

                    // Step 5: The exception is passed to the caller
                    throw tre;
                }//end of if (tre != null)
    } //end of invoke method