From b283911134c7bcbe83288f07fb0afeefb9f9280f Mon Sep 17 00:00:00 2001
From: Matteo Cherubini <cherubinimatte@gmail.com>
Date: Fri, 8 May 2026 21:09:42 +0200
Subject: [PATCH] feat: Add scripts for linting genomes and adding individual
 genomes

---
 scripts/add-genome.sh   | 29 +++++++++++++++++++++++++++++
 scripts/lint-genomes.sh | 38 ++++++++++++++++++++++++++++++++++++++
 2 files changed, 67 insertions(+)
 create mode 100644 scripts/add-genome.sh
 create mode 100644 scripts/lint-genomes.sh

diff --git a/scripts/add-genome.sh b/scripts/add-genome.sh
new file mode 100644
index 0000000..09e0aa1
--- /dev/null
+++ b/scripts/add-genome.sh
@@ -0,0 +1,29 @@
+#!/usr/bin/env bash
+# =============================================================================
+# scripts/add-genome.sh
+# Helper to add a single new genome to the existing infrastructure.
+# Usage: make add-genome NAME=my-new-genome DESC="Description here"
+# =============================================================================
+
+set -euo pipefail
+source "lib/output.sh"
+source "config.env"
+
+GENOME_NAME="${1:-}"
+GENOME_DESC="${2:-}"
+
+if [[ -z "$GENOME_NAME" || -z "$GENOME_DESC" ]]; then
+    error "Missing arguments."
+    echo "Usage: $0 <genome-name> <description>"
+    exit 1
+fi
+
+step "Adding New Genome: ${GENOME_NAME}"
+
+# Overwrite the GENOMES array for this session to process only the new one
+export GENOMES=("${GENOME_NAME}|${GENOME_DESC}")
+
+# Trigger the standard genome setup logic
+bash "scripts/setup-genomes.sh"
+
+success "Genome '${GENOME_NAME}' added and linked successfully!"
diff --git a/scripts/lint-genomes.sh b/scripts/lint-genomes.sh
new file mode 100644
index 0000000..1aad8f4
--- /dev/null
+++ b/scripts/lint-genomes.sh
@@ -0,0 +1,38 @@
+#!/usr/bin/env bash
+# =============================================================================
+# scripts/lint-genomes.sh
+# Executes quality control across all registered genomes.
+# =============================================================================
+
+set -euo pipefail
+source "lib/output.sh"
+source "config.env"
+source "lib/lint.sh"
+
+step "Starting Knowledge Genome Linting"
+
+TOTAL_ERRORS=0
+
+# Iterate through genome submodules inside the Master repo
+for genome_dir in "${WORK_DIR}/${MASTER_REPO}"/genome-*/; do
+    [[ -d "$genome_dir" ]] || continue
+
+    GENOME_NAME=$(basename "$genome_dir")
+    info "Auditing genome: ${GENOME_NAME}..."
+
+    # Find all .md files, excluding AGENTS.md and external references
+    while IFS= read -r md_file; do
+        # Run validations
+        lint_markdown_file "$md_file" "$GENOME_NAME" || TOTAL_ERRORS=$((TOTAL_ERRORS + $?))
+        check_privacy_consistency "$md_file" || TOTAL_ERRORS=$((TOTAL_ERRORS + $?))
+        check_broken_links "$md_file"
+
+    done < <(find "$genome_dir" -name "*.md" ! -name "AGENTS.md" ! -path "*/core-karpathy/*")
+done
+
+if [[ $TOTAL_ERRORS -eq 0 ]]; then
+    success "Linting passed: All files are consistent and secure."
+else
+    error "Linting failed: Found ${TOTAL_ERRORS} critical issues."
+    exit 1
+fi