Pass file path of each doc reference in references returned by API

- Pass file path of reference along with the compiled reference in
  list of references returned by chat API converts
- Update the structure of references from list of strings to list of
  dictionary (containing 'compiled' and 'file' keys)
- Pull out the compiled reference from the new references data struct
  wherever it was is being used

src/interface/obsidian/src/chat_view.ts

@@ -247,7 +247,8 @@ export class KhojChatView extends KhojPaneView {
         return referenceButton;
     }
 
-    generateReference(messageEl: Element, reference: string, index: number) {
+    generateReference(messageEl: Element, referenceJson: any, index: number) {
+        let reference: string = referenceJson.hasOwnProperty("compiled") ? referenceJson.compiled : referenceJson;
         // Escape reference for HTML rendering
         let escaped_ref = reference.replace(/"/g, """)