parse_env_flag <- function(name, default = FALSE) {
  value <- Sys.getenv(name, unset = if (default) "true" else "false")
  tolower(trimws(value)) %in% c("1", "true", "yes", "y")
}

find_replication_root <- function() {
  file_arg <- grep("^--file=", commandArgs(FALSE), value = TRUE)
  script_dir <- character()
  if (length(file_arg) > 0) {
    script_path <- sub("^--file=", "", file_arg[[1]])
    script_dir <- dirname(normalizePath(script_path, mustWork = FALSE))
  }

  candidates <- unique(Filter(
    nzchar,
    c(
      Sys.getenv("IMAGEDECONFOUND_REPLICATION_ROOT", unset = ""),
      getwd(),
      dirname(getwd()),
      dirname(dirname(getwd())),
      script_dir,
      dirname(script_dir)
    )
  ))

  for (candidate in candidates) {
    candidate <- normalizePath(candidate, winslash = "/", mustWork = FALSE)
    if (!dir.exists(candidate)) {
      next
    }
    if (file.exists(file.path(candidate, "code", "lib", "call_CI_Conf_5k_3yr.R")) &&
        dir.exists(file.path(candidate, "data", "interim")) &&
        dir.exists(file.path(candidate, "results"))) {
      return(candidate)
    }
  }

  stop("Could not locate the replication root. Set IMAGEDECONFOUND_REPLICATION_ROOT explicitly.")
}

set_replication_root <- function(root = NULL, quiet = FALSE) {
  root <- normalizePath(root %||% find_replication_root(), winslash = "/", mustWork = FALSE)
  options(replication.root = root)
  setwd(root)
  if (!quiet) {
    message("Replication root: ", root)
  }
  invisible(root)
}

`%||%` <- function(lhs, rhs) {
  if (is.null(lhs) || length(lhs) == 0) {
    return(rhs)
  }
  lhs
}

bundle_results_root <- function(root = getOption("replication.root")) {
  file.path(root, "results", "per_run_csv", "Epoch5EarlyStopNewTreatDefLabelS_Run2")
}

bundle_results_processed_dir <- function(root = getOption("replication.root")) {
  file.path(bundle_results_root(root), "results_processed")
}

bundle_public_results_dir <- function(root = getOption("replication.root")) {
  file.path(root, "results", "processed")
}

bundle_tables_dir <- function(root = getOption("replication.root")) {
  file.path(root, "tables")
}

ensure_dir <- function(path) {
  dir.create(path, recursive = TRUE, showWarnings = FALSE)
  invisible(path)
}

resolve_external_path <- function(envvar, default_relative) {
  root <- getOption("replication.root", default = find_replication_root())
  env_value <- Sys.getenv(envvar, unset = "")
  if (nzchar(env_value)) {
    return(normalizePath(env_value, winslash = "/", mustWork = FALSE))
  }
  normalizePath(file.path(root, default_relative), winslash = "/", mustWork = FALSE)
}

run_replication_script <- function(script_relative, overrides = list()) {
  root <- set_replication_root(quiet = TRUE)
  script_path <- file.path(root, script_relative)
  if (!file.exists(script_path)) {
    stop("Missing script: ", script_path)
  }

  keep_names <- unique(c(
    names(overrides),
    get0("KeepObjectsAcrossAnalysisStrings", ifnotfound = character(), inherits = TRUE)
  ))

  env <- new.env(parent = globalenv())
  if (length(overrides) > 0) {
    list2env(overrides, envir = env)
  }
  env$KeepObjectsAcrossAnalysisStrings <- keep_names

  sys.source(script_path, envir = env)
  invisible(env)
}

copy_named_files <- function(files, destination_dir, overwrite = TRUE) {
  ensure_dir(destination_dir)
  if (length(files) == 0) {
    return(invisible(character()))
  }

  ok <- file.copy(files, destination_dir, overwrite = overwrite)
  if (any(!ok)) {
    failed <- basename(files[!ok])
    warning("Some files failed to copy: ", paste(failed, collapse = ", "))
  }
  invisible(files[ok])
}

sync_results_processed <- function(overwrite = TRUE) {
  source_dir <- bundle_results_processed_dir()
  destination_dir <- bundle_public_results_dir()

  if (!dir.exists(source_dir)) {
    warning("No nested results_processed directory found at ", source_dir)
    return(invisible(character()))
  }

  files <- list.files(source_dir, full.names = TRUE)
  copied <- copy_named_files(files, destination_dir, overwrite = overwrite)
  message("Synced ", length(copied), " processed result files into results/processed.")
  invisible(copied)
}

sync_table_assets <- function(overwrite = TRUE) {
  results_dir <- bundle_public_results_dir()
  tables_dir <- bundle_tables_dir()
  tex_files <- list.files(results_dir, pattern = "\\.tex$", full.names = TRUE)
  copied <- copy_named_files(tex_files, tables_dir, overwrite = overwrite)
  if (length(copied) > 0) {
    message("Synced ", length(copied), " LaTeX table/macro files into tables/.")
  }
  invisible(copied)
}

compute_sha256 <- function(path) {
  sha256sum_bin <- Sys.which("sha256sum")
  shasum_bin <- Sys.which("shasum")

  if (nzchar(sha256sum_bin)) {
    output <- system2(sha256sum_bin, shQuote(path), stdout = TRUE, stderr = TRUE)
    return(strsplit(output[[1]], "\\s+")[[1]][[1]])
  }
  if (nzchar(shasum_bin)) {
    output <- system2(shasum_bin, c("-a", "256", shQuote(path)), stdout = TRUE, stderr = TRUE)
    return(strsplit(output[[1]], "\\s+")[[1]][[1]])
  }
  NA_character_
}

verify_manifest_file <- function(manifest_path, verify_hash = TRUE) {
  if (!file.exists(manifest_path)) {
    message("Manifest not found at ", manifest_path, ". Skipping checksum verification.")
    return(invisible(NULL))
  }

  manifest <- read.csv(manifest_path, stringsAsFactors = FALSE)
  required_columns <- c("path", "size_bytes", "sha256", "role")
  missing_columns <- setdiff(required_columns, names(manifest))
  if (length(missing_columns) > 0) {
    stop("Manifest is missing columns: ", paste(missing_columns, collapse = ", "))
  }

  root <- getOption("replication.root", default = find_replication_root())
  resolved_paths <- file.path(root, manifest$path)
  exists_flag <- file.exists(resolved_paths)
  if (!all(exists_flag)) {
    stop(
      "Manifest references missing files: ",
      paste(manifest$path[!exists_flag], collapse = ", ")
    )
  }

  actual_sizes <- file.info(resolved_paths)$size
  if (!all(actual_sizes == manifest$size_bytes)) {
    bad_rows <- which(actual_sizes != manifest$size_bytes)
    stop(
      "Manifest size mismatch for: ",
      paste(manifest$path[bad_rows], collapse = ", ")
    )
  }

  if (verify_hash) {
    sample_hash <- compute_sha256(resolved_paths[[1]])
    if (is.na(sample_hash)) {
      message("No SHA-256 utility found. Skipping checksum verification.")
      return(invisible(manifest))
    }

    actual_hashes <- vapply(resolved_paths, compute_sha256, character(1))
    if (!all(actual_hashes == manifest$sha256)) {
      bad_rows <- which(actual_hashes != manifest$sha256)
      stop(
        "Manifest checksum mismatch for: ",
        paste(manifest$path[bad_rows], collapse = ", ")
      )
    }
  }

  message("Manifest verification passed for ", nrow(manifest), " files.")
  invisible(manifest)
}

verify_bundle <- function(verify_hash = TRUE) {
  root <- set_replication_root(quiet = TRUE)

  required_dirs <- c(
    "code/lib",
    "data/interim",
    "data/country_regions",
    "results/per_run_csv/Epoch5EarlyStopNewTreatDefLabelS_Run2",
    "results/processed",
    "figures/manuscript",
    "tables",
    "env",
    "manifests"
  )
  required_files <- c(
    "README.md",
    "code/common.R",
    "code/00_verify_bundle.R",
    "code/01_rebuild_paper_outputs.R",
    "code/02_run_main_ate_optional.R",
    "code/03_run_within_unit_robustness.R",
    "code/04_consolidate_results.R",
    "code/05_build_figures_tables.R",
    "data/interim/dhs_5k_confounders.csv",
    "data/interim/dhs_treated_sector_3yr.csv",
    "data/interim/africa_oda_sector_group.csv",
    "results/processed/ICA_xruns_all_vt_emb_3yr_2013.csv",
    "results/processed/wb_vs_ch_sector_scatter_WithinUnitVar.pdf",
    "env/R_packages.txt",
    "env/requirements-image-download.txt",
    "manifests/external_requirements.md"
  )

  missing_dirs <- required_dirs[!dir.exists(file.path(root, required_dirs))]
  missing_files <- required_files[!file.exists(file.path(root, required_files))]
  if (length(missing_dirs) > 0 || length(missing_files) > 0) {
    problems <- c(
      if (length(missing_dirs) > 0) paste("Missing directories:", paste(missing_dirs, collapse = ", ")),
      if (length(missing_files) > 0) paste("Missing files:", paste(missing_files, collapse = ", "))
    )
    stop(paste(problems, collapse = " | "))
  }

  expected_run_counts <- c(
    vt_3yr_noX = 99L,
    vt_3yr_onlyFE = 100L,
    vt_3yr_onlyX = 100L,
    vt_3yr_onlyXandFE = 100L,
    vt_3yr_withFE = 100L,
    vt_3yr_withX = 400L,
    vt_3yr_withXandFE = 100L,
    vt_3yr_unitFE = 100L,
    vt_3yr_did = 49L
  )

  run_root <- bundle_results_root(root)
  actual_run_counts <- vapply(
    names(expected_run_counts),
    function(name) {
      length(list.files(file.path(run_root, name), pattern = "\\.csv$", full.names = TRUE))
    },
    integer(1)
  )

  if (any(actual_run_counts < expected_run_counts)) {
    bad <- names(actual_run_counts)[actual_run_counts < expected_run_counts]
    stop(
      "Incomplete per-run CSV directories: ",
      paste(
        sprintf("%s (%s < %s)", bad, actual_run_counts[bad], expected_run_counts[bad]),
        collapse = ", "
      )
    )
  }

  results_processed_n <- length(list.files(bundle_public_results_dir(root), full.names = TRUE))
  if (results_processed_n < 100L) {
    stop("results/processed looks incomplete: found only ", results_processed_n, " files.")
  }

  manuscript_fig_n <- length(list.files(file.path(root, "figures", "manuscript"), full.names = TRUE))
  if (manuscript_fig_n < 100L) {
    stop("figures/manuscript looks incomplete: found only ", manuscript_fig_n, " files.")
  }

  verify_manifest_file(
    file.path(root, "manifests", "file_manifest.csv"),
    verify_hash = verify_hash
  )

  summary <- list(
    root = root,
    per_run_csv_counts = actual_run_counts,
    results_processed_n = results_processed_n,
    manuscript_fig_n = manuscript_fig_n
  )

  message("Bundle verification passed.")
  invisible(summary)
}