diff --git a/codex-plonky2-circuits/README.md b/codex-plonky2-circuits/README.md
index 7c6f9be..14e94f0 100644
--- a/codex-plonky2-circuits/README.md
+++ b/codex-plonky2-circuits/README.md
@@ -5,9 +5,7 @@ This crate is an implementation of the [codex storage proofs circuits](https://g
 
 ## Code organization
 
-- [`merkle_safe`](./src/merkle_tree/merkle_safe.rs) is the implementation of "safe" merkle tree used in codex, consistent with the one [here](https://github.com/codex-storage/nim-codex/blob/master/codex/merkletree/merkletree.nim).
-
-- [`merkle_circuit`](./src/circuits/merkle_circuit) is the Plonky2 Circuit implementation of "safe" merkle tree above.
+- [`merkle_circuit`](./src/circuits/merkle_circuit) is the Plonky2 Circuit implementation of "safe" merkle tree.
 
 - [`sample_cells`](./src/circuits/sample_cells.rs) is the Plonky2 Circuit implementation for sampling cells in dataset merkle tree.
 
diff --git a/proof-input/README.md b/proof-input/README.md
index fefb426..2dae891 100644
--- a/proof-input/README.md
+++ b/proof-input/README.md
@@ -4,11 +4,13 @@ WARNING: This is a work-in-progress prototype, and has not received careful code
 This crate generates input to the proof circuit based on the test parameters. The proof input generated can be ported into
 the [`plonky2 codex proof circuits`](../codex-plonky2-circuits). Currently only generates fake data for testing.
 
-## Code organization
+## Code organization 
+
+- [`merkle_tree`](./src/merkle_tree) is the implementation of "safe" merkle tree used in codex, consistent with the one [here](https://github.com/codex-storage/nim-codex/blob/master/codex/merkletree/merkletree.nim).
 
 - [`gen_input`](./src/gen_input.rs) contains the necessary function to generate the proof input. 
 
-- [`json`](./src/json.rs) contains the serialization function to read and write the proof input from/to json files. 
+- [`json`](./src/serialization) contains the serialization functions to read and write the proof input from/to json files. 
 
 - [`params`](./src/params.rs) is the test parameters used to generate the input. The params include circuit params as well.
 
diff --git a/workflow/README.md b/workflow/README.md
index 30cf91e..af55a91 100644
--- a/workflow/README.md
+++ b/workflow/README.md
@@ -65,10 +65,10 @@ export NCELLS=512         # Number of cells in this slot
 Alternatively, for testing you can just use the default parameters as follows:
 
 ```rust
-use proof_input::params::TestParams;
+use proof_input::params::Params;
 
 fn main() {
-    let params = TestParams::<F,D>::default();
+    let params = Params::default();
 }
 ```
 #### Step 2: Run the Script