The path to the Piwik index.php is hardcoded in piwik/misc/cron/archive.sh and therefore needs to be adapted to the correct location everytime I update.
This should be solved in a more user-friendly way.
For portability, paths in cron scripts are absolute. If PIWIK_PATH were to be defined in some other config file, the path to this config file would also be an absolute path. Thus, archive.sh would (still) have to be updated each time.
Workaround: rename your locally modified archive.sh and use that file in your crontab. Thus, it won't be overwritten when you update/upgrade Piwik.
A fix has been committed for #599 which determines the Piwik path.