Update documentation to remove manage_externals

The README no longer references manage_externals

README.md

@@ -13,18 +13,17 @@ This collaborative effort aims to simplify the user experience of running diagno
 To install CUPiD, you need to check out the code and then set up a few environments.
 The initial examples have hard-coded paths that require you to be on `casper`.
 
-The code relies on submodules to install `manage_externals` and then uses `manage_externals` for a few packages that are still being developed,
-so the `git clone` process is a little more complicated than usual:
+The code relies on submodules to install a few packages that are still being developed,
+so the `git clone` process requires `--recurse-submodules`:
 
 ``` bash
 $ git clone --recurse-submodules https://github.com/NCAR/CUPiD.git
-$ cd CUPiD
-$ ./manage_externals/checkout_externals
 ```
 
-Then build the necessary conda environments with
+Then `cd` into the `CUPiD` directory and build the necessary conda environments with
 
 ``` bash
+$ cd CUPiD
 $ mamba env create -f environments/dev-environment.yml
 $ conda activate cupid-dev
 $ which cupid-run
@@ -37,7 +36,7 @@ Notes:
 It still feels slower than running `mamba` directly, hence the recommendation to install with `mamba env create` rather than `conda env create`.
 If you do not have `mamba` installed, you can still use `conda`... it will just be significantly slower.
 (To see what version of conda you have installed, run `conda --version`.)
-1. If `./manage_externals/checkout_externals` is not found, run `git submodule update --init` to clone the submodule.
+1. If `externals/ADF` and `externals/mom6-tools` are empty, run `git submodule update --init` to clone the submodules.
 1. If `which cupid-run` returned the error `which: no cupid-run in ($PATH)`, then please run the following:
 
    ``` bash