tools: remove unneeded dependency files

The new version of dmn more effectively cleans unneeded dependency
files. (Thanks, BridgeAR!) It's now in the udpate-*.sh files but run it
manually to get the benefits now (and to have a smaller diff when we
update).

PR-URL: https://github.com/nodejs/node/pull/27730


Reviewed-By: Michaël Zasso <targos@protonmail.com>
Reviewed-By: Ruben Bridgewater <ruben@bridgewater.de>
Reviewed-By: Yongsheng Zhang <zyszys98@gmail.com>
Reviewed-By: Roman Reiss <me@silverwind.io>
Reviewed-By: Luigi Pinca <luigipinca@gmail.com>