#!/usr/bin/env bash
# =============================================================================
# scripts/verify-genomes.sh
# Check (default) or --sync the directory structure of every registered genome
# against the canonical layout in lib/structure.sh.
#
#   bash scripts/verify-genomes.sh           # report drift, non-zero exit on drift
#   bash scripts/verify-genomes.sh --sync    # create missing dirs everywhere (safe)
#
# No hardware/LLM involved — pure structure check. Run anywhere.
# =============================================================================
set -euo pipefail
source "lib/output.sh"
source "globals.env"
source "registry.sh"
source "lib/structure.sh"

MODE="verify"
[[ "${1:-}" == "--sync" ]] && MODE="sync"

step "Genome structure: ${MODE}"

TOTAL_MISSING=0
for entry in "${GENOMES[@]}"; do
  IFS='|' read -r GENOME_NAME _ <<< "$entry"       # 4-field registry; only GENOME_NAME used here
  genome_dir="${WORK_DIR}/${MASTER_REPO}/${GENOME_NAME}"

  if [[ ! -d "$genome_dir" ]]; then
    warn "not found locally, skipping: ${GENOME_NAME}"
    continue
  fi

  info "Genome: ${GENOME_NAME}"
  if [[ "$MODE" == "sync" ]]; then
    structure_sync "$genome_dir"
  else
    structure_report "$genome_dir" && m=0 || m=$?
    TOTAL_MISSING=$((TOTAL_MISSING + m))
  fi
done

echo ""
if [[ "$MODE" == "sync" ]]; then
  success "Structure sync complete."
elif [[ $TOTAL_MISSING -eq 0 ]]; then
  success "Structure verified: all genomes match the canonical layout."
else
  error "Structure drift: ${TOTAL_MISSING} missing directory(ies). Fix with: make sync-structure"
  exit 1
fi