From 92e68fff00f6da3ed56053ea58952da77db42b2b Mon Sep 17 00:00:00 2001
From: Matteo Cherubini <cherubinimatte@gmail.com>
Date: Sat, 9 May 2026 11:34:21 +0200
Subject: [PATCH] feat: Integrate knowledge decay checks into lint-genomes
 script

---
 scripts/lint-genomes.sh | 45 ++++++++++++++++++++++++++++++-----------
 1 file changed, 33 insertions(+), 12 deletions(-)

diff --git a/scripts/lint-genomes.sh b/scripts/lint-genomes.sh
index 1aad8f4..392fac7 100644
--- a/scripts/lint-genomes.sh
+++ b/scripts/lint-genomes.sh
@@ -2,6 +2,8 @@
 # =============================================================================
 # scripts/lint-genomes.sh
 # Executes quality control across all registered genomes.
+# Iterates from the GENOMES registry in config.env — not from filesystem patterns —
+# so all genomes are covered regardless of their naming convention.
 # =============================================================================
 
 set -euo pipefail
@@ -12,27 +14,46 @@ source "lib/lint.sh"
 step "Starting Knowledge Genome Linting"
 
 TOTAL_ERRORS=0
+TOTAL_STALE=0
 
-# Iterate through genome submodules inside the Master repo
-for genome_dir in "${WORK_DIR}/${MASTER_REPO}"/genome-*/; do
-    [[ -d "$genome_dir" ]] || continue
+for entry in "${GENOMES[@]}"; do
+    IFS='|' read -r GENOME_NAME _ <<< "$entry"
+    genome_dir="${WORK_DIR}/${MASTER_REPO}/${GENOME_NAME}"
+
+    if [[ ! -d "$genome_dir" ]]; then
+        warn "Genome directory not found locally, skipping: ${genome_dir}"
+        continue
+    fi
 
-    GENOME_NAME=$(basename "$genome_dir")
     info "Auditing genome: ${GENOME_NAME}..."
 
-    # Find all .md files, excluding AGENTS.md and external references
+    # Lint all .md files except AGENTS.md and core-karpathy reference
     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 + $?))
+
+        lint_markdown_file "$md_file" "$GENOME_NAME"
+        file_errors=$?
+        TOTAL_ERRORS=$((TOTAL_ERRORS + file_errors))
+
+        check_privacy_consistency "$md_file"
+        TOTAL_ERRORS=$((TOTAL_ERRORS + $?))
+
+        check_knowledge_decay "$md_file"
+        stale=$?
+        TOTAL_STALE=$((TOTAL_STALE + stale))
+
         check_broken_links "$md_file"
 
-    done < <(find "$genome_dir" -name "*.md" ! -name "AGENTS.md" ! -path "*/core-karpathy/*")
+    done < <(find "$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."
+echo ""
+if [[ $TOTAL_ERRORS -eq 0 && $TOTAL_STALE -eq 0 ]]; then
+    success "Linting passed: all files are consistent, secure, and current."
+elif [[ $TOTAL_ERRORS -eq 0 && $TOTAL_STALE -gt 0 ]]; then
+    warn "Linting passed with ${TOTAL_STALE} stale file(s). Review and re-validate flagged pages."
 else
-    error "Linting failed: Found ${TOTAL_ERRORS} critical issues."
+    error "Linting failed: ${TOTAL_ERRORS} critical issue(s), ${TOTAL_STALE} stale file(s)."
     exit 1
 fi