diff --git a/scripts/setup-genomes.sh b/scripts/setup-genomes.sh
new file mode 100644
index 0000000..4de8ed8
--- /dev/null
+++ b/scripts/setup-genomes.sh
@@ -0,0 +1,62 @@
+#!/usr/bin/env bash
+# =============================================================================
+# scripts/setup-genomes.sh
+# Iterates through the GENOMES registry to provision remote and local repos.
+# Handles git-crypt initialization and submodule linking.
+# =============================================================================
+
+set -euo pipefail
+source "lib/output.sh"
+source "config.env"
+source "lib/scaffold.sh"
+source "lib/git-crypt.sh"
+source "providers/${PROVIDER}.sh"
+
+step "Processing Genome Registry"
+
+for entry in "${GENOMES[@]}"; do
+    # Parse name and description from the array
+    IFS='|' read -r GENOME_NAME GENOME_DESC <<< "$entry"
+    export GENOME_NAME GENOME_DESC
+
+    info "Processing: ${GENOME_NAME}..."
+
+    # 1. Remote Provisioning (Idempotent: skips if exists)
+    provider_create_repo "${GENOME_NAME}" "${GENOME_DESC}" "true"
+
+    GENOME_PATH="${WORK_DIR}/${MASTER_REPO}/${GENOME_NAME}"
+
+    if [ ! -d "${GENOME_PATH}" ]; then
+        info "Creating local directory and initializing scaffold..."
+        mkdir -p "${GENOME_PATH}"
+        cd "${GENOME_PATH}"
+        git init
+
+        # IMPORTANT: Initialize git-crypt BEFORE creating sensitive files
+        gcrypt_init
+
+        # Create directory structure and apply templates
+        scaffold_genome "."
+        install_precommit_hook "."
+
+        # Initial commit and push to remote
+        git add .
+        git commit -m "feat: initial scaffold for ${GENOME_NAME}"
+
+        SSH_URL=$(provider_ssh_url "${GENOME_NAME}")
+        git remote add origin "${SSH_URL}"
+        git push -u origin main
+
+        # Export the AES key for the user to back up
+        gcrypt_export_key "${GENOME_NAME}"
+
+        # 2. Link as submodule in the Master repository
+        cd "${WORK_DIR}/${MASTER_REPO}"
+        info "Linking ${GENOME_NAME} as a submodule..."
+        git submodule add "${SSH_URL}" "${GENOME_NAME}"
+        git add .gitmodules "${GENOME_NAME}"
+        git commit -m "feat: link submodule ${GENOME_NAME}"
+    else
+        warn "Genome directory '${GENOME_NAME}' already exists. Skipping local setup."
+    fi
+done
diff --git a/scripts/setup-master.sh b/scripts/setup-master.sh
new file mode 100644
index 0000000..7d9bf6f
--- /dev/null
+++ b/scripts/setup-master.sh
@@ -0,0 +1,34 @@
+#!/usr/bin/env bash
+# =============================================================================
+# scripts/setup-master.sh
+# Initializes the umbrella (Master) repository and core configurations.
+# =============================================================================
+
+set -euo pipefail
+source "lib/output.sh"
+source "config.env"
+source "lib/scaffold.sh"
+
+step "Configuring Master Repository: ${MASTER_REPO}"
+
+# Ensure workspace exists
+mkdir -p "${WORK_DIR}/${MASTER_REPO}"
+cd "${WORK_DIR}/${MASTER_REPO}"
+
+if [ ! -d ".git" ]; then
+    info "Initializing Git in Master repository..."
+    git init
+
+    # Optional: Add Karpathy's core reference as a read-only submodule
+    if [ -n "${GIST_URL:-}" ]; then
+        info "Adding core-karpathy as an external reference..."
+        git submodule add "${GIST_URL}" core-karpathy || warn "Could not add core-karpathy submodule."
+    fi
+fi
+
+# Apply master-level templates (README, AGENTS)
+scaffold_master "."
+
+# Initial commit for the master structure
+git add .
+git commit -m "chore: initialize master scaffold" || info "No changes to commit in master."