Update Nokogiri to v1.12.5

This addresses a CVE that is only relevant to JRuby users
(https://github.com/sparklemotion/nokogiri/blob/main/CHANGELOG.md), but
this gem is still flagged by security scanners.

Some other dependency updates:

* ruby-magic https://my.diffend.io/gems/ruby-magic/0.4.0/0.5.3
* racc diff: https://my.diffend.io/gems/racc/1.5.2/1.6.0
* mini_portile2: https://my.diffend.io/gems/mini_portile2/2.5.0/2.6.1

Changelog: changed