breakpoints_flush_caches unintentionally invoked by system_cron

hook_flush_caches gets unintentionally invoked on system_cron() as well as drupal_flush_all_caches(). As a result, it regenerates breakpoints and kills menu and theme caches for all themes enabled every single time.

This is a major issue for sites that have cron running every minute and even if you use cron managers, this still gets invoked because it's called in system_cron function.

While breakpoint regeneration is needed and should be regenerated on actual cache clean, this also gets invoked on settings form submit and on system_cron.

For breakpoints to be regenerated, this module has implemented hook_flush_caches, but it collides with this part of system_cron function.

$core = array('cache', 'cache_path', 'cache_filter', 'cache_page', 'cache_form', 'cache_menu');
  $cache_tables = array_merge(module_invoke_all('flush_caches'), $core);
  foreach ($cache_tables as $table) {
    cache_clear_all(NULL, $table);
  }

The only way to distinguish where it is invoked, we are must trace code execution and run this code only when it's run trough drupal_flush_all_caches function (this function is called by both UI cache clean and drush cc all, so it's safe). This approach is also used by memcache module for slightly different purpose and is related to issue http://drupal.org/node/81461

Stack trace for breakpoints_flush_caches:
$trace[3] drupal_flush_all_caches
$trace[3] system_cron

This is proposed solution for breakpoints_flush_caches function, will attach patch shortly:

$backtrace = debug_backtrace();
  if (isset($backtrace[3]) && ($backtrace[3]['function'] == 'drupal_flush_all_caches') && empty($backtrace[3]['args'])) {