diff --git a/Makefile b/Makefile
index 26c149c..cfd4537 100644
--- a/Makefile
+++ b/Makefile
@@ -30,16 +30,17 @@ setup:
 add-genome:
 	@if [ -z "$(NAME)" ] || [ -z "$(DESC)" ]; then \
 		echo "Error: NAME and DESC are required."; \
-		echo "Usage: make add-genome NAME=my-genome DESC='My description' [LINKED=owner/project-repo]"; \
+		echo "Usage: make add-genome NAME=my-genome DESC='My description' [LINKED=owner/project-repo] [CROSS=yes|no]"; \
 		exit 1; \
 	fi
-	@bash scripts/add-genome.sh "$(NAME)" "$(DESC)" "$(LINKED)"
+	@bash scripts/add-genome.sh "$(NAME)" "$(DESC)" "$(LINKED)" "$(or $(CROSS),no)"
 
 status:
+	@[ -d "$(MASTER_REPO)" ] || { echo "Master non trovato. Esegui 'make setup'."; exit 1; }
 	@echo "--- Master Status ---"
-	@git submodule status
+	@cd $(MASTER_REPO) && git submodule status
 	@echo "--- Encryption Status (per genome) ---"
-	@git submodule foreach 'git-crypt status 2>/dev/null | head -n 10 || true'
+	@cd $(MASTER_REPO) && git submodule foreach 'git-crypt status 2>/dev/null | head -n 10 || true'
 
 verify-structure:
 	@bash scripts/verify-genomes.sh
@@ -62,14 +63,16 @@ doctor:
 	@echo "System ready."
 
 sync:
+	@[ -d "$(MASTER_REPO)" ] || { echo "Master non trovato. Esegui 'make setup'."; exit 1; }
 	@echo "Syncing submodules..."
-	@git submodule update --init --recursive
+	@cd $(MASTER_REPO) && git submodule update --init --recursive
 	@echo "--- Unpushed commits per genome ---"
-	@git submodule foreach 'git log --oneline @{u}.. 2>/dev/null | head -5 || true'
+	@cd $(MASTER_REPO) && git submodule foreach 'git log --oneline @{u}.. 2>/dev/null | head -5 || true'
 
 lock:
+	@[ -d "$(MASTER_REPO)" ] || { echo "Master non trovato. Esegui 'make setup'."; exit 1; }
 	@echo "Locking master repository..."
-	@git-crypt lock 2>/dev/null || true
+	@cd $(MASTER_REPO) && git-crypt lock 2>/dev/null || true
 	@echo "Locking all submodules..."
-	@git submodule foreach 'git-crypt lock 2>/dev/null || true'
+	@cd $(MASTER_REPO) && git submodule foreach 'git-crypt lock 2>/dev/null || true'
 	@echo "All genomes securely locked."
diff --git a/README.md b/README.md
index 01aadb1..f682de4 100644
--- a/README.md
+++ b/README.md
@@ -692,7 +692,9 @@ If a key is lost or compromised:
 ```bash
 # From the knowledge-genome-orchestrator/ directory
 source lib/git-crypt.sh
-cd ~/knowledge-genome-orchestrator/genome-dev
+# If gcrypt_rotate_key operates on the CWD: cd into .../master-knowledge-genome/genome-dev
+# If it navigates by name instead:          cd into .../master-knowledge-genome
+cd ~/knowledge-genome-orchestrator/master-knowledge-genome
 gcrypt_rotate_key "genome-dev"
 ```
 
diff --git a/registry.sh b/registry.sh
index 2c20200..3083cad 100644
--- a/registry.sh
+++ b/registry.sh
@@ -12,7 +12,7 @@ _REGISTRY_LOADED=1
 PROJECT_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 
 # Dynamic paths
-WORK_DIR="${HOME}/knowledge-genome-orchestrator"
+WORK_DIR="${PROJECT_ROOT}"
 KEYS_DIR="${WORK_DIR}/keys"
 TEMPLATES_DIR="${PROJECT_ROOT}/templates"
 LIB_DIR="${PROJECT_ROOT}/lib"