diff --git a/Makefile b/Makefile
index af1f923..1d8010e 100644
--- a/Makefile
+++ b/Makefile
@@ -1,5 +1,5 @@
 # =============================================================================
-# Knowledge Genome - Makefile v. 1.2.1
+# Knowledge Genome - Makefile v. 1.2.2
 # Orchestrates the setup and management of the knowledge base.
 # =============================================================================
 
diff --git a/lib/scaffold.sh b/lib/scaffold.sh
index 8c1e3a7..330d53a 100644
--- a/lib/scaffold.sh
+++ b/lib/scaffold.sh
@@ -64,8 +64,11 @@ scaffold_genome() {
 
 install_precommit_hook() {
   local repo_path="$1"
-  local hook_path="${repo_path}/.git/hooks/pre-commit"
+  local hooks_dir
+  hooks_dir="$(git -C "$repo_path" rev-parse --git-path hooks)"
+  local hook_path="${hooks_dir}/pre-commit"
 
+  mkdir -p "$hooks_dir"
   cp "${TEMPLATES_DIR}/pre-commit.sh" "$hook_path"
   chmod +x "$hook_path"
   success "Pre-commit security hook installed at: $hook_path"
diff --git a/scripts/setup-genomes.sh b/scripts/setup-genomes.sh
index 354ab12..a2d8c77 100644
--- a/scripts/setup-genomes.sh
+++ b/scripts/setup-genomes.sh
@@ -40,6 +40,8 @@ for entry in "${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}"