how do I get the workitems fixed between build results snapshots? using java api

The generateChangeLog Ant task can do this.  Its source is in the SDK, in .../plugins/com.ibm.team.build.toolkit.rtc.feature.source_3.0.700.v20131019_0328/src/com.ibm.team.build.toolkit_3.0.700.v20131015_0229/ant_tasks/build-antsrc.zip

This seems to work

    public String[] compareSnapshots(IBuildResult result,IBaselineSetHandle new_baselineSetHandle) throws TeamRepositoryException {
        ITeamBuildClient buildClient = (ITeamBuildClient) repo.getClientLibrary(ITeamBuildClient.class);
        IWorkspaceManager wm = SCMPlatform.getWorkspaceManager(repo);
        IItemManager itemManager = repo.itemManager();
        List workItemUUIDs = new ArrayList();
        List<IChangeSet> changesets = new ArrayList();
        IBaselineSetHandle last_snapshot_handle = null;
        
        // Get Last Result snapshot
        IBuildResultContribution[] last_contribution = buildClient.getBuildResultContributions(result,ScmConstants.EXTENDED_DATA_TYPE_ID_BUILD_SNAPSHOT,MONITOR);        
        for (int i = 0; i < last_contribution.length; i++) {
            last_snapshot_handle = (IBaselineSetHandle) last_contribution[i].getExtendedContribution();
        }
        
        // Compare snapshots
        IChangeHistorySyncReport report = wm.compareBaselineSets(last_snapshot_handle,new_baselineSetHandle,Collections.EMPTY_LIST,MONITOR);        
        
        // Get Outgoing changesets
        if (report.outgoingChangeSets().size() > 0) {
            changesets.addAll(itemManager.fetchCompleteItems(report.outgoingChangeSets(), IItemManager.DEFAULT, null));
        }
        
        // Get Incomming changsets
        if (report.incomingChangeSets().size() > 0) {            
            changesets.addAll(itemManager.fetchCompleteItems(report.incomingChangeSets(), IItemManager.DEFAULT, null));
        }

        // Check Changeset for workitems
        if (changesets.size() != 0) {
            
            // Get summary of chageset links
            List<IChangeSetLinkSummary> links = wm.getChangeSetLinkSummary(changesets,MONITOR);
            for (Iterator it = links.iterator(); it.hasNext();) {
                IChangeSetLinkSummary link = (IChangeSetLinkSummary) it.next();
                
                // Get Link handles
                List<ILinkHandle> links_handles = link.getLinks();
                for (Iterator it1 = links_handles.iterator(); it1.hasNext();) {
                    ILinkHandle links_handle = (ILinkHandle) it1.next();
                    ILink links_item = (ILink)repo.itemManager().fetchCompleteItem(links_handle, IItemManager.DEFAULT, MONITOR);

                    // Get Work Item from link handle
                    IReference targetRef = links_item.getTargetRef();
                    if (targetRef.isItemReference() && ((IItemReference) targetRef).getReferencedItem() instanceof IWorkItemHandle) {
 
                        IWorkItemHandle workItemHandle = (IWorkItemHandle) ((IItemReference) targetRef).getReferencedItem();
                        workItemUUIDs.add(workItemHandle.getItemId().getUuidValue());
                    }
                }
            }
        }
        
        // Convert Work Item list to array
        String[] handleIds = new String[workItemUUIDs.size()];
        int i = 0;
        for (Iterator it = workItemUUIDs.iterator(); it.hasNext();) {
            handleIds[i] = (String) it.next();
            i++;
        }
        
        return handleIds;
    }