lib/scaffold.sh

@@ -64,11 +64,8 @@ scaffold_genome() {
 
 install_precommit_hook() {
   local repo_path="$1"
-  local hooks_dir
+  local hook_path="${repo_path}/.git/hooks/pre-commit"
-  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"

scripts/setup-genomes.sh

@@ -40,8 +40,6 @@ for entry in "${GENOMES[@]}"; do
 
         cd "${GENOME_NAME}"
 
-        git switch -C main
-
         # IMPORTANT: Initialize git-crypt BEFORE creating any files
         gcrypt_init
 
@@ -52,12 +50,9 @@ for entry in "${GENOMES[@]}"; do
         git add .
         git commit -m "feat: initial scaffold and git-crypt init for ${GENOME_NAME}"
 
-        git push -u origin main
+        git branch -M main
 
-        cd "${WORK_DIR}/${MASTER_REPO}"
+        git push -u origin main
-        git add .gitmodules "${GENOME_NAME}"
-        git commit -m "chore: register submodule ${GENOME_NAME}"
-        git push
 
         # Key export and instructions
         gcrypt_export_key "${GENOME_NAME}"