fix: add file: prefix to org-mode links for Emacs resolution

Emorg org-mode requires [[file:path]] syntax for file links to be
clickable. Updated both extract.mjs and scaffold-notes.mjs generators,
and fixed all 200 existing note files.

org/study_deck_02/dsa/trees/0226-invert-binary-tree.org

@@ -1,7 +1,7 @@
 * TODO 0226. Invert Binary Tree :easy:
 #+PROPERTY: STUDY_DECK_02
 :PROPERTIES:
-:NEETCODE: [[../../roadmap.org::*0226. Invert Binary Tree][Roadmap]]
+:NEETCODE: [[file:../../roadmap.org::*0226. Invert Binary Tree][Roadmap]]
 :END:
 
 ** TODO Approach