fix: use full update path when --custom-source is passed with --yes (#2336)

* fix: use full update path when --custom-source is passed with --yes

When --yes is used on an existing install, the installer auto-selects
quick-update. However, quick-update never re-clones custom module repos
— it only reads whatever is already in the cache. This means
--custom-source with a new version tag (e.g. @1.1.0) is silently
ignored and the previously cached version (e.g. 1.0.1) is reported as
"already up to date".

Default to the full update path when --custom-source is present, so the
custom repo gets re-cloned at the requested version. Also ensure all
installed modules are included in the selection when --yes is combined
with --custom-source, preventing previously installed modules from being
removed.

* fix: address review feedback on choices.find() and comment clarity

* style: prettier fix for empty-body methods in custom-module-manager

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Co-authored-by: Brian <bmadcode@gmail.com>