From 813924460dcbcd34ab4b3b3906829af939c6de64 Mon Sep 17 00:00:00 2001
From: Matteo Cherubini <cherubinimatte@gmail.com>
Date: Fri, 12 Jun 2026 12:16:17 +0200
Subject: [PATCH 1/3] feat: Improve pre-commit hook installation robustness

---
 lib/scaffold.sh | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

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"

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 2/3] 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}"

From 3e8af163c0670db2d5fc35886b4a524fe9318a39 Mon Sep 17 00:00:00 2001
From: Matteo Cherubini <cherubinimatte@gmail.com>
Date: Fri, 12 Jun 2026 12:17:11 +0200
Subject: [PATCH 3/3] Update version

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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.
 # =============================================================================