Clarifications in readme and example config

Author: julianxcarter

README.md

@@ -213,6 +213,8 @@ The mCODE Extraction Framework uses the node `csv-parse` library to parse specif
   },
 ```
 
+**Note:** The mCODE Extraction Framework enables the `bom`, `skip_empty_lines`, and `skip_lines_with_empty_values` options by default, including these options in the configuration file will cause these default options to be overwritten.
+
 ## Terminology and Architecture
 
 This framework consists of three key components: Extractors, Modules and Templates. Below is, in order:

config/csv.config.example.json

@@ -1,12 +1,7 @@
 {
   "patientIdCsvPath": "Users/YourAccount/absolute/path/to/patient-mrns.csv",
   "commonExtractorArgs": {
-    "dataDirectory": "Users/YourAccount/absolute/path/to/data/directory",
-    "csvParse": {
-      "options": {
-        "bom": true
-      }
-    }
+    "dataDirectory": "Users/YourAccount/absolute/path/to/data/directory"
   },
   "notificationInfo": {
     "host": "smtp.example.com",