update table of contents

Author: KatarinaYuan

README.md

@@ -47,12 +47,26 @@ This repository contains the refactored runtime used for large-scale pretraining
 - [Updates](#updates)
 - [File Structure](#file-structure)
 - [Installation](#installation)
+  - [Option A: Conda/Mamba environment for `src` (recommended on cluster)](#option-a-condamamba-environment-for-src-recommended-on-cluster)
+  - [Option B: venv](#option-b-venv)
 - [General Configuration](#general-configuration)
 - [Download](#download)
-- [Model Checkpoints](#model-checkpoints)
-- [Datasets](#datasets)
+  - [Dataset](#dataset)
+  - [Checkpoint](#checkpoint)
 - [Setup](#setup)
-- [Command Cookbook](#command-cookbook)
+  - [Quick Start](#quick-start)
+  - [Entrypoints](#entrypoints)
+  - [Shared CLI Blocks](#shared-cli-blocks)
+  - [Scenario Index](#scenario-index)
+    - [1.1) From Scratch on PBMC](#11-from-scratch-on-pbmc)
+    - [1.2) From Scratch on Tahoe100M](#12-from-scratch-on-tahoe100m)
+    - [1.3) From Scratch on Replogle](#13-from-scratch-on-replogle)
+    - [2.1) Sampling on PBMC (from checkpoint; PBMC as an example)](#21-sampling-on-pbmc-from-checkpoint-pbmc-as-an-example)
+    - [3) Pretraining](#3-pretraining)
+    - [4.1) Finetuning on PBMC](#41-finetuning-on-pbmc)
+    - [4.2) Finetuning on Tahoe100M](#42-finetuning-on-tahoe100m)
+    - [4.3) Finetuning on Replogle](#43-finetuning-on-replogle)
+  - [Notes](#notes)
 - [Citation](#citation)
 
 ## Feature

index.html

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