cleanup makefiles and original readme

docs/make.bat

-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=source
-set BUILDDIR=build
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.https://www.sphinx-doc.org/
-	exit /b 1
-)
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
-popd

docs/source/index.md

@@ -107,4 +107,5 @@ Training_OpenFold.md
 :caption: Reference 
 Aux_seq_files.md
 OpenFold_Parameters.md
+original_readme.md
 ```
\ No newline at end of file

docs/source/README.md → docs/source/original_readme.md

-![header ](imgs/of_banner.png)
-_Figure: Comparison of OpenFold and AlphaFold2 predictions to the experimental structure of PDB 7KDX, chain B._
-
-
-# OpenFold
+# Original OpenFold README 
 
 A faithful but trainable PyTorch reproduction of DeepMind's 
 [AlphaFold 2](https://github.com/deepmind/alphafold).
 
 ## Contents
 
-- [OpenFold](#openfold)
-  - [Contents](#contents)
+- [OpenFold]
+  - [Contents]
   - [Features](#features)
   - [Installation (Linux)](#installation-linux)
   - [Download Alignment Databases](#download-alignment-databases)