diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..d1279d2
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,36 @@
+# =============================================================================
+# Knowledge Genome - Makefile
+# Orchestrates the setup and management of the knowledge base.
+# =============================================================================
+
+include config.env
+export $(shell sed 's/=.*//' config.env)
+
+.PHONY: setup add-genome status lint clean help
+
+help:
+	@echo "Available commands:"
+	@echo "  make setup         - Full system initialization"
+	@echo "  make add-genome    - Register and scaffold a new genome"
+	@echo "  make status        - Check submodule and encryption status"
+	@echo "  make lint          - Verify schema, privacy flags, and metadata"
+
+lint:
+	@bash scripts/lint-genomes.sh
+
+setup:
+	@bash scripts/setup.sh
+
+add-genome:
+	@if [ -z "$(NAME)" ] || [ -z "$(DESC)" ]; then \
+		echo "Error: NAME and DESC are required."; \
+		echo "Usage: make add-genome NAME=my-genome DESC='My description'"; \
+		exit 1; \
+	fi
+	@bash scripts/add-genome.sh "$(NAME)" "$(DESC)"
+
+status:
+	@echo "--- Master Status ---"
+	@git submodule status
+	@echo "--- Encryption Status (First 10 files) ---"
+	@git-crypt status | head -n 10
diff --git a/scripts/setup.sh b/scripts/setup.sh
new file mode 100644
index 0000000..eb2e5b7
--- /dev/null
+++ b/scripts/setup.sh
@@ -0,0 +1,36 @@
+#!/usr/bin/env bash
+# =============================================================================
+# scripts/setup.sh
+# Main entry point for the Knowledge Genome framework initialization.
+# Orchestrates dependency checks, master repo setup, and genome provisioning.
+# =============================================================================
+
+set -euo pipefail
+
+# Resolve script directory and source core components
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+source "${SCRIPT_DIR}/lib/output.sh"
+source "${SCRIPT_DIR}/config.env"
+source "${SCRIPT_DIR}/lib/deps.sh"
+
+step "Starting Knowledge Genome Setup"
+
+# 1. Environment and Dependency Validation
+info "Validating system dependencies..."
+check_deps
+check_git_identity
+
+# 2. Master Repository Provisioning
+info "Initializing Master Repository..."
+bash "${SCRIPT_DIR}/scripts/setup-master.sh"
+
+# 3. Genomes Provisioning (as defined in config.env)
+info "Provisioning registered Genomes..."
+bash "${SCRIPT_DIR}/scripts/setup-genomes.sh"
+
+success "Setup process completed successfully!"
+
+box "Next Steps:" \
+    "1. Navigate to master: cd ${WORK_DIR}/${MASTER_REPO}" \
+    "2. Secure your keys: Upload contents of ${KEYS_DIR} to Vaultwarden" \
+    "3. Start building: Add files to raw/articles/ and run your agents"