Fix missing examples tab for profiles + fix csv escaping problem + fi…

…x problem ignoring existing narrative ie provided

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/Publisher.java

@@ -1249,7 +1249,7 @@ public void createIg() throws Exception, IOException, EOperationOutcome, FHIRExc
           new DependencyRenderer(pcm, outputDir, npmName, templateManager, dependencyList, context, markdownEngine, rc, specMaps).render(publishedIg, true, false, false), new HTAAnalysisRenderer(context, outputDir, markdownEngine).render(publishedIg.getPackageId(), fileList, publishedIg.present()),
           new PublicationChecker(repoRoot, historyPage, markdownEngine, findReleaseLabelString()).check(), renderGlobals(), copyrightYear, context, scanForR5Extensions(), modifierExtensions,
           generateDraftDependencies(),
-          noNarrativeResources, noValidateResources, validationOff, generationOff, dependentIgFinder, context.getTxClientManager());
+          noNarrativeResources, noValidateResources, validationOff, generationOff, dependentIgFinder, context.getTxClientManager(), versionProblems);
       val.setValidationFlags(hintAboutNonMustSupport, anyExtensionsAllowed, checkAggregation, autoLoad, showReferenceMessages, noExperimentalContent, displayWarnings);
       tts.end();
       if (isChild()) {
@@ -4131,6 +4131,7 @@ private void loadIGPackage(String name, String canonical, String packageId, Stri
     specMaps.add(igm);
     if (!VersionUtilities.versionsCompatible(version, igm.getVersion())) {
       if (!pi.isWarned()) {
+        versionProblems.add("This IG is version "+version+", while the IG '"+pi.name()+"' is from version "+igm.getVersion());
         log("Version mismatch. This IG is version "+version+", while the IG '"+pi.name()+"' is from version "+igm.getVersion()+" (will try to run anyway)");
         pi.setWarned(true);   
       }
@@ -4187,6 +4188,7 @@ public void loadFromPackage(String name, String canonical, NpmPackage pi, String
             } else {
               if (!VersionUtilities.versionsCompatible(version, pi.fhirVersion())) {
                 if (!pi.isWarned()) {
+                  versionProblems.add("This IG is for FHIR version "+version+", while the package '"+pi.name()+"#"+pi.version()+"' is for FHIR version "+pi.fhirVersion());
                   log("Version mismatch. This IG is for FHIR version "+version+", while the package '"+pi.name()+"#"+pi.version()+"' is for FHIR version "+pi.fhirVersion()+" (will ignore that and try to run anyway)");
                   pi.setWarned(true);
                 }
@@ -7683,11 +7685,10 @@ private void generate() throws Exception {
     }
     logMessage("Generate Summaries");
 
-    genBasePages();
-
     if (!changeList.isEmpty()) {
       generateSummaryOutputs(db);
     }
+    genBasePages();
     db.closeUp();
     TextFile.bytesToFile(extensionTracker.generate(), Utilities.path(tempDir, "usage-stats.json"));
     try {
@@ -9143,7 +9144,7 @@ private void saveCSList(String name, List<CodeSystem> cslist, DBBuilder db, int
     JsonArray items = new JsonArray();
     json.add("codeSystems", items);
 
-    b.append("URL,Version,Status,OIDs,Name,Title,Descriptino,Used\r\n");
+    b.append("URL,Version,Status,OIDs,Name,Title,Description,Used\r\n");
 
     for (CodeSystem cs : cslist) {
 
@@ -9195,9 +9196,9 @@ private void saveCSList(String name, List<CodeSystem> cslist, DBBuilder db, int
       b.append(",");
       b.append(oids.isEmpty() ? "" : "\""+CommaSeparatedStringBuilder.join(",", oids)+"\"");
       b.append(",");
-      b.append(cs.getName());
+      b.append(Utilities.escapeCSV(cs.getName()));
       b.append(",");
-      b.append(cs.getTitle());
+      b.append(Utilities.escapeCSV(cs.getTitle()));
       b.append(",");
       b.append("\""+Utilities.escapeCSV(cs.getDescription())+"\"");
       b.append(",");
@@ -9285,9 +9286,9 @@ private void saveVSList(String name, List<ValueSet> vslist, DBBuilder db, int vi
       b.append(",");
       b.append(oids.isEmpty() ? "" : "\""+CommaSeparatedStringBuilder.join(",", oids)+"\"");
       b.append(",");
-      b.append(vs.getName());
+      b.append(Utilities.escapeCSV(vs.getName()));
       b.append(",");
-      b.append(vs.getTitle());
+      b.append(Utilities.escapeCSV(vs.getTitle()));
       b.append(",");
       b.append("\""+Utilities.escapeCSV(vs.getDescription())+"\"");
       b.append(",");
@@ -11145,6 +11146,8 @@ private String processRefTag(DBBuilder db, String src, FetchedFile f) {
   private LanguageUtils langUtils;
 
   private boolean simplifierMode;
+
+  private List<String> versionProblems = new ArrayList<>();
 
   private String processSQLCommand(DBBuilder db, String src, FetchedFile f) throws FHIRException, IOException {
     long start = System.currentTimeMillis();
@@ -12003,7 +12006,7 @@ private void generateHtml(FetchedFile f, FetchedResource r, Map<String, String>
     XhtmlComposer xc = new XhtmlComposer(XhtmlComposer.XML, module.isNoNarrative());
     if (igpkp.wantGen(r, "html")) {
       long start = System.currentTimeMillis();
-      XhtmlNode xhtml = (lang == null || lang.equals(r.getElement().getNamedChildValue("language"))) ? null : getXhtml(f, r);
+      XhtmlNode xhtml = (lang == null || lang.equals(r.getElement().getNamedChildValue("language"))) ? getXhtml(f, r) : null;
       if (xhtml == null && HistoryGenerator.allEntriesAreHistoryProvenance(r.getElement())) {
         RenderingContext ctxt = lrc.copy(false).setParser(getTypeLoader(f, r));
         List<ProvenanceDetails> entries = loadProvenanceForBundle(igpkp.getLinkFor(r, true), r.getElement(), f);