From eeafddbf1ad696fa6046690a23e8f85f31371ab9 Mon Sep 17 00:00:00 2001
From: Matteo Cherubini <cherubinimatte@gmail.com>
Date: Fri, 12 Jun 2026 12:16:17 +0200
Subject: [PATCH] feat: Automatically register new genomes as submodules

---
 scripts/setup-genomes.sh | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/scripts/setup-genomes.sh b/scripts/setup-genomes.sh
index 354ab12..a2d8c77 100644
--- a/scripts/setup-genomes.sh
+++ b/scripts/setup-genomes.sh
@@ -40,6 +40,8 @@ for entry in "${GENOMES[@]}"; do
 
         cd "${GENOME_NAME}"
 
+        git switch -C main
+
         # IMPORTANT: Initialize git-crypt BEFORE creating any files
         gcrypt_init
 
@@ -50,10 +52,13 @@ for entry in "${GENOMES[@]}"; do
         git add .
         git commit -m "feat: initial scaffold and git-crypt init for ${GENOME_NAME}"
 
-        git branch -M main
-
         git push -u origin main
 
+        cd "${WORK_DIR}/${MASTER_REPO}"
+        git add .gitmodules "${GENOME_NAME}"
+        git commit -m "chore: register submodule ${GENOME_NAME}"
+        git push
+
         # Key export and instructions
         gcrypt_export_key "${GENOME_NAME}"
         gcrypt_print_key_instructions "${GENOME_NAME}"