change the mis-leading README.md

The readme says it is Markdown but actually HTML
Also each section is messy

Author: MyEnthusiastic

auto-run-nondex/README.md

@@ -1,22 +1,25 @@
-# `runNondex`
 
-This script runs individual modules in the specified project with the `Nondex` tool and shows results automatically in the `markdown` format.
+What repo we want to run Nondex on?
 
-Output file is located inside the project folder and called `report_md.md` The output would only contain tests that are detected by the nondex tool as flaky, and the result includes the seeds used for the test and the status of the test result.
+1. This repo has not appeared in the latest `pr-data.csv`
+2. This repo contains pom.xml file.
 
-All the log information would be stored inside the `.runNondex` folder inside the project. 
 
-Inside the `.runNondex` folder: 
-- `./LOGSSS` contains nondex logs for all submodules.
-- `LOGresult` contains a list of file paths that contain test errors.
-- `htmlOutput` contains a list of file paths for the HTML files generated by the nondex tool.
+
+
+# runNondexAll
+
+This is simplified script for quick start
+Go to folder of .pom.xml files, and check all the result in result.log
+
+
+# Dependencies
 
 It is recommended to use a virtual python environment for the required modules:
 ```bash
 python3 -m venv <path_to_the_new_virtual_environment>
 source <path_to_the_new_virtual_environment>/bin/activate
 ```
-
 Make sure to first install packages in `requirements.txt`.
 
 ```bash
@@ -25,26 +28,22 @@ cd auto-run-nondex
 pip install -r requirements.txt
 ```
 
-# `runNondexUnderAuthor`
-
-This script runs all the valid repos under a given author using the `runNondex` script above. 
-
-The valid repo is defined as:
+# runNondex in each module:
+```bash
+./runNondex.sh <project_folder_path> <optional-directory-name>
+```
 
-1. This repo has not appeared in the latest `pr-data.csv`
-2. This repo contains pom.xml file.
+With the second parameter in `./runNondex.sh`, you can only run Nondex on modules in a certain directory instead of the entire project.
 
 
+# runNondexUnderAuthor
 
 
-### Usage:
 ```bash
-./runNondex.sh <project_folder_path> <optional-directory-name>
 ./runNondexUnderAuthor.sh <author_repository_url> <path_where_you_want_to_clone_those repos>
 ```
 
-With the second parameter in `./runNondex.sh`, you can only run Nondex on modules in a certain directory instead of the entire project.
-
+How to find the Author?
 
 >  To find the author_repository_url, find the author that you want to run Nondex with, and get this author's repository overview url (e.g., https://github.com/orgs/spotify/repositories). Note that you don't need to provide the url with other parameters, as the script will automatically add the parameters needed.
 >
@@ -65,3 +64,10 @@ With the second parameter in `./runNondex.sh`, you can only run Nondex on module
 >  `find . -maxdepth 1 -type d \( ! -name . \) -exec bash -c "cd '{}' &&  git rev-parse HEAD && git config --get remote.origin.url | rev | cut -c5- | rev  && cat .runNondex/htmlOutput && cat report_md.md" \; &> progress_stats.md`
 
 
+# Folder structure
+
+All the log information would be stored inside the `.runNondex` folder inside the project.
+
+- `./modulelog` contains nondex logs for all submodules.
+- `result` contains a list of file paths that contain test errors.
+- `htmlOutput` contains a list of file paths for the HTML files generated by the nondex tool.