move illustrative code into old folders, more udpates to memory code

circuits/cpu/src/main.nr

@@ -2,4 +2,7 @@
 fn main(
 ) {
 
+    //This is going to be where we put procedure 5
+    // For procedures see notes/recursion.md
+
 }

circuits/memory/src/continuation.nr

@@ -25,6 +25,8 @@ fn run(
     hashpath_a: [Field; 12], //we hash all the reads 
     hashpath_b: [Field; 12], //for the writes
 ) -> Field {
+    //TODO: account for padding in the addr_sorted and op_sorted values
+
     //hash the mem_page
     let leaf: [Field; 2] = std::hash::pedersen(mem_page);
     //prove merkle inclusion

circuits/memory/src/main.nr

@@ -37,6 +37,9 @@ fn main(
     hashpath_a: [Field; 12], //we hash all the reads 
     hashpath_b: [Field; 12], //for the writes
     ) -> (Field, Field, Field, Field) {
+        // These two only for testing purposes
+        // For procedures see notes/recursion.md
+
         // PROCEDURE 1.a
         // let challenges_and_partial_permutations = memcheck::run(
         //     addr_sorted_step,
@@ -60,7 +63,7 @@ fn main(
         //     r, mem_root_a, mem_root_b, page_index, hashpath_a, hashpath_b);
 
 
-        //PROCEDURE 4 (aggregation step as comments)
+        //PROCEDURE 4 (aggregation step as comments) main memory can be use for aggregation?
         // verify continuations and memcheck
         // aggregated permutation 1_b = product([partial_permutation])
         // aggregated permutation 1_a_addr = product([challenges_and_partial_permutations[2]])

circuits/memory/src/memcheck.nr

@@ -14,6 +14,8 @@ fn run(
     // returns the two intermediary permutation checks, and two intermediary challenge hashes
 ) -> [Field; 4] {
 
+    //TODO: account for padding in the addr_sorted and op_sorted values
+
     // compute the intermediary challenge (we aggregate this at the end to double check the 'r' value)
     let mut challenge_a = 0;
     let mut challenge_op = 0;