diff --git a/Makefile b/Makefile
index 09243a7..8e9441c 100644
--- a/Makefile
+++ b/Makefile
@@ -1,22 +1,25 @@
 # =============================================================================
-# Knowledge Genome - Makefile v. 1.0.0
+# Knowledge Genome - Makefile v. 1.1.0
 # Orchestrates the setup and management of the knowledge base.
 # =============================================================================
 
 include globals.env
 export $(shell grep -v '^[#[:space:]]' globals.env | sed 's/=.*//')
 
-.PHONY: setup add-genome status lint lock doctor sync help
+.PHONY: setup add-genome status lint lock doctor sync test verify-structure sync-structure help
 
 help:
 	@echo "Available commands:"
-	@echo "  make setup         - Full system initialization"
-	@echo "  make add-genome    - Register and scaffold a new genome"
-	@echo "  make status        - Check submodule and encryption status"
-	@echo "  make lint          - Verify schema, privacy flags, and metadata"
-	@echo "  make lock          - Lock all encrypted files across all genomes"
-	@echo "  make doctor        - Verify all required tools are installed"
-	@echo "  make sync          - Sync submodules and report unpushed commits"
+	@echo "  make setup            - Full system initialization"
+	@echo "  make add-genome       - Register and scaffold a new genome [LINKED=owner/repo]"
+	@echo "  make status           - Check submodule and encryption status"
+	@echo "  make lint             - Verify schema, privacy flags, and metadata"
+	@echo "  make verify-structure - Report directory drift across all genomes"
+	@echo "  make sync-structure   - Create any missing canonical dirs (safe)"
+	@echo "  make test             - Run the bats test suite (no LLM/GPU needed)"
+	@echo "  make lock             - Lock all encrypted files across all genomes"
+	@echo "  make doctor           - Verify all required tools are installed"
+	@echo "  make sync             - Sync submodules and report unpushed commits"
 
 lint:
 	@bash scripts/lint-genomes.sh
@@ -27,16 +30,26 @@ 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'"; \
+		echo "Usage: make add-genome NAME=my-genome DESC='My description' [LINKED=owner/project-repo]"; \
 		exit 1; \
 	fi
-	@bash scripts/add-genome.sh "$(NAME)" "$(DESC)"
+	@bash scripts/add-genome.sh "$(NAME)" "$(DESC)" "$(LINKED)"
 
 status:
 	@echo "--- Master Status ---"
 	@git submodule status
-	@echo "--- Encryption Status (First 10 files) ---"
-	@git-crypt status | head -n 10
+	@echo "--- Encryption Status (per genome) ---"
+	@git submodule foreach 'git-crypt status 2>/dev/null | head -n 10 || true'
+
+verify-structure:
+	@bash scripts/verify-genomes.sh
+
+sync-structure:
+	@bash scripts/verify-genomes.sh --sync
+
+test:
+	@command -v bats >/dev/null 2>&1 || { echo "  MISSING: bats (sudo apt install bats)"; exit 1; }
+	@bats tests/
 
 doctor:
 	@echo "Checking required tools..."
@@ -45,6 +58,7 @@ doctor:
 	@command -v curl       >/dev/null 2>&1 || { echo "  MISSING: curl";       exit 1; }
 	@command -v jq         >/dev/null 2>&1 || { echo "  MISSING: jq";         exit 1; }
 	@command -v bw         >/dev/null 2>&1 || echo "  OPTIONAL: bw (Bitwarden CLI) not found — key injection will be manual."
+	@command -v python3    >/dev/null 2>&1 || echo "  OPTIONAL: python3 not found — needed for 'make test' and the ingest skill (index-append.py), not for setup."
 	@echo "System ready."
 
 sync:
diff --git a/skills/ingest/references/frontmatter.md b/skills/ingest/references/frontmatter.md
deleted file mode 100644
index e69de29..0000000