docs: added directory docs and yaml config doc file #9

docs/index.md

@@ -43,7 +43,6 @@ The tool supports verification and mapping across diagnostic coding formats belo
 
 ### **Phenotype directory structure
 
-```markdown
 ```
 workspace/                          # Default workspace directory
 ├── phen/                           # Default phenotype directory
@@ -54,14 +53,13 @@ workspace/                          # Default workspace directory
 │   ├── omop/                        # Processed phenotype concept sets in OMOP database CSV files
 │   ├── config.yaml                  # Phenotype configuration file
 │   ├── vocab_versions.yaml          # Versions file for vocabularies used to generate concept sets
-```
-```  
+``` 
 
 ### **Configuration File**
 
 Phenotype configuration is stored in the root of the phenotype directory in `config.yaml`. The file is yaml format. 
 
-#### **Root Element**  
+#### **Root Phenotype Element**  
 - `phenotype`: **(object)** The root element containing all phenotype-related concept sets and metadata.
 
 #### **Phenotype Attributes**