Remove references from docs and other files to deleted crates

[jeffcharles]

Description of the change

Removing references to deleted crates from docs and various files.

Why am I making this change?

For the docs, it'll be at best confusing and at worst a waste of time for anyone reading them when they realize they're out of date. So IMHO better to remove them now and then add the up-to-date details later when the project is more stable.

For the other files, the outdated references might cause confusion later.

Checklist

• I've updated the relevant CHANGELOG files if necessary. Changes to javy-cli and javy-core do not require updating CHANGELOG files.
• I've updated the relevant crate versions if necessary. Versioning policy for library crates
• I've updated documentation including crate documentation if necessary.