From 96041daefdda4de04a82a385ce78624a4076bb60 Mon Sep 17 00:00:00 2001
From: Teagan King <98482480+TeaganKing@users.noreply.github.com>
Date: Tue, 15 Oct 2024 15:03:53 -0600
Subject: [PATCH 1/2] Update README.md to include note on git submodule
 'gotcha'

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 668ac8b..41f17a9 100644
--- a/README.md
+++ b/README.md
@@ -37,6 +37,7 @@ It still feels slower than running `mamba` directly, hence the recommendation to
 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 the subdirectories in `externals/` are all empty, run `git submodule update --init` to clone the submodules.
+1. For existing users who cloned `CUPiD` prior to the switch from manage externals to git submodule, we recommend removing `externals/` before checking out main, running `git submodule update`, and removing `manage_externals` (if it is still present after `git submodule update --init`).
 1. If `which cupid-run` returned the error `which: no cupid-run in ($PATH)`, then please run the following:
 
    ``` bash

From 530fe92e942eedccb6e43faab3c7cf3ee32cb3a6 Mon Sep 17 00:00:00 2001
From: Teagan King <98482480+TeaganKing@users.noreply.github.com>
Date: Wed, 16 Oct 2024 13:39:17 -0600
Subject: [PATCH 2/2] Update README.md to include 'init'

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 41f17a9..5197308 100644
--- a/README.md
+++ b/README.md
@@ -37,7 +37,7 @@ It still feels slower than running `mamba` directly, hence the recommendation to
 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 the subdirectories in `externals/` are all empty, run `git submodule update --init` to clone the submodules.
-1. For existing users who cloned `CUPiD` prior to the switch from manage externals to git submodule, we recommend removing `externals/` before checking out main, running `git submodule update`, and removing `manage_externals` (if it is still present after `git submodule update --init`).
+1. For existing users who cloned `CUPiD` prior to the switch from manage externals to git submodule, we recommend removing `externals/` before checking out main, running `git submodule update --init`, and removing `manage_externals` (if it is still present after `git submodule update --init`).
 1. If `which cupid-run` returned the error `which: no cupid-run in ($PATH)`, then please run the following:
 
    ``` bash