#!/usr/bin/env bash
# =============================================================================
# scripts/lint-genomes.sh
# Executes quality control across all registered genomes.
# Iterates from the GENOMES registry in registry.sh — not from filesystem patterns —
# so all genomes are covered regardless of their naming convention.
# =============================================================================

set -euo pipefail
source "lib/output.sh"
source "globals.env"
source "registry.sh"
source "lib/lint.sh"

step "Starting Knowledge Genome Linting"

TOTAL_ERRORS=0
TOTAL_STALE=0

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

    info "Auditing genome: ${GENOME_NAME}..."

    # Lint all .md files except AGENTS.md and core-karpathy reference
    while IFS= read -r md_file; do

        lint_markdown_file "$md_file" "$GENOME_NAME" && fe=0   || fe=$?
        check_privacy_consistency "$md_file"          && pce=0  || pce=$?
        check_page_size "$md_file"                    && pse=0  || pse=$?
        TOTAL_ERRORS=$((TOTAL_ERRORS + fe + pce + pse))

        check_knowledge_decay "$md_file"              && stale=0 || stale=$?
        TOTAL_STALE=$((TOTAL_STALE + stale))

        check_broken_links "$md_file" || true   # warnings only, never contributes to errors

    done < <(find "$genome_dir" -name "*.md" \
                ! -name "AGENTS.md" \
                ! -path "*/core-karpathy/*")
done

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: ${TOTAL_ERRORS} critical issue(s), ${TOTAL_STALE} stale file(s)."
    exit 1
fi