diff --git a/app/dashboard/documents/[id]/page.tsx b/app/dashboard/documents/[id]/page.tsx
index efe15c2..7309060 100644
--- a/app/dashboard/documents/[id]/page.tsx
+++ b/app/dashboard/documents/[id]/page.tsx
@@ -68,7 +68,7 @@ export default async function DocumentPage(props: { params: { id: string } }) {
 
   const processedContent = await remark()
     .use(remarkHtml)
-    .process(pages.join(" "));
+    .process(pages.join("\n"));
 
   return (
     <SidebarProvider>
diff --git a/app/dashboard/upload/page.tsx b/app/dashboard/upload/page.tsx
index 9ccf45b..38cfa4a 100644
--- a/app/dashboard/upload/page.tsx
+++ b/app/dashboard/upload/page.tsx
@@ -30,7 +30,7 @@ export default async function Page() {
 
   const { data: documents, error } = await supabase
     .from("documents")
-    .select("id, file_name, created_at, owner")
+    .select("id, file_name, created_at, owner, is_processing")
     .eq("owner", user.id)
     .order("created_at", { ascending: false });
 
@@ -44,6 +44,7 @@ export default async function Page() {
       <AppSidebar
         documents={documents.map((d) => {
           return {
+            disabled: d.is_processing,
             name: d.file_name,
             url: `/dashboard/documents/${d.id}`,
             emoji: "📄",
diff --git a/bun.lockb b/bun.lockb
index da4b3e2..bacc2ec 100755
Binary files a/bun.lockb and b/bun.lockb differ
diff --git a/components/UploadZone.tsx b/components/UploadZone.tsx
index c148a2b..a373914 100644
--- a/components/UploadZone.tsx
+++ b/components/UploadZone.tsx
@@ -49,7 +49,7 @@ export default function UploadZone({ user }: { user?: { id: string } }) {
 
     eventSource.addEventListener("error", (event) => {
       console.error("SSE Error:", event);
-      toast.error("An error occurred while processing the document.", {
+      toast.error("An error occurred while processing the document", {
         description: event.data || "Unknown error",
       });
       setUploading(false);
diff --git a/components/nav-favorites.tsx b/components/nav-favorites.tsx
index d1eaf4a..ddaa4c6 100644
--- a/components/nav-favorites.tsx
+++ b/components/nav-favorites.tsx
@@ -4,6 +4,7 @@ import {
   ArrowUpRight,
   FileText,
   Link,
+  LoaderCircle,
   MoreHorizontal,
   StarOff,
   Trash2,
@@ -30,6 +31,7 @@ export function NavDocuments({
   documents,
 }: {
   documents: {
+    disabled?: boolean;
     name: string;
     url: string;
     emoji?: string;
@@ -42,10 +44,14 @@ export function NavDocuments({
       <SidebarGroupLabel>Documents</SidebarGroupLabel>
       <SidebarMenu>
         {documents.map((item) => (
-          <SidebarMenuItem key={item.name}>
-            <SidebarMenuButton asChild>
+          <SidebarMenuItem key={item.name} aria-disabled={item.disabled}>
+            <SidebarMenuButton asChild disabled={item.disabled}>
               <a href={item.url} title={item.name}>
-                <span>{item.emoji ? item.emoji : <FileText />}</span>
+                {item.disabled ? (
+                  <LoaderCircle className="animate-spin text-muted-foreground" />
+                ) : (
+                  <span>{item.emoji ? item.emoji : <FileText />}</span>
+                )}
                 <span>{item.name}</span>
               </a>
             </SidebarMenuButton>
diff --git a/supabase/functions/process-document.ts b/supabase/functions/process-document/index.ts
similarity index 89%
rename from supabase/functions/process-document.ts
rename to supabase/functions/process-document/index.ts
index 5103b76..d1388fe 100644
--- a/supabase/functions/process-document.ts
+++ b/supabase/functions/process-document/index.ts
@@ -20,18 +20,27 @@ Do not return the Markdown as a code block, only as a raw string, without any ne
 
 No data or information should ever be removed, it should only be processed and formatted.
 
-There are in-text citations/references in the text, remove them from the text and put them into an object where the key is the reference number and the value is the text.
+There are in-text citations/references in the text, remove them from the text (**but most importantly, keep the reference number in the text. use a <sup></sup> tag**) and put them into an object where the key is the reference number and the value is the text.
 
-The Markdown should be human-readable and well-formatted.
+The Markdown should be human-readable and well-formatted. The markdown string should properly sanitized and should not break a JSON parser when returned as the final format.
+
+Return the final result as a text object with the following structure (without code block formatting):
+
+"""
+<processed markdown text>
+
+---------
 
-Return the final result as a JSON object with the following structure:
 {
-  "markdown": "<processed_markdown>",
   "citations": {
-    "1": "<citation_text_1>",
-    "2": "<citation_text_2>"
+    "1": "Citation text for reference 1",
+    "2": "Citation text for reference 2",
+    // ... more citations
   }
 }
+"""
+
+Do not return the text object as a code block, only as a raw string.
 `;
 Deno.serve(async (req) => {
   if (req.method === "OPTIONS") {
@@ -276,16 +285,22 @@ Deno.serve(async (req) => {
           }
 
           if (response.choices[0].message.content) {
-            const markdownResponse = JSON.parse(
-              response.choices[0].message.content.toString()
+            // remove any potential code block formatting from the content
+            console.log(
+              `[${page.index}] ${response.choices[0].message.content}`
             );
-            const citations = markdownResponse.citations;
-            const markdown = markdownResponse.markdown;
+            const split =
+              response.choices[0].message.content.split("---------");
+
+            const content = split[0].trim();
+            const citationsStr = split[1]?.trim() || "{}";
+            const citations = JSON.parse(citationsStr).citations || {};
+
             console.log("Generating Markdown for page:", page.index);
             sendEvent("status", {
               message: `Generating Markdown for page ${page.index}`,
             });
-            const markdown = replaceImagesInMarkdown(markdown, imageData);
+            const markdown = replaceImagesInMarkdown(content, imageData);
 
             return {
               ...page,