Installing and upgrading help

First, some history background:
For production deployment we've generated RPM's of moodle and modules that we need. Trying to deploy those RPMs into testing environment we found out that they have overlaping files (same file belongs to two packages).
Offending packages so far:
moodle_book
moodle_CAS
moodle

For example moodle_book contains files
lang/ca/help/index.html lang/ca/help/mods.html lang/de/book.php lang/es/book.php lang/id/help/mods.html lang/ja/book.php lang/ja/help/index.html lang/ja/help/mods.html

that overwrite original files from moodle itself. What's the rule of thumb in those situations or in other words - what's the established best practice?