Test the REPL with the Scala 3 REPL rather than Ammonite

[Gedochao]

Is your feature request related to a problem? Please describe.
We currently test a number of things in our REPL integration tests using Ammonite (see #3209).
As Scala CLI is closely tied with Scala 3 releases and Ammonite is maintained separately, we should uncouple these 2 things.
The way things are, it's hard to guess what works until there's an Ammonite version for a given Scala version ready (which sometimes happens late or not at all, like with Scala 3.4.0/3.4.1)

Describe the solution you'd like
We should test all repl sub-command features via the Scala 3 REPL rather than Ammonite REPL.
The only tests relying on Ammonite should be the ones testing the actual integration.

We should run all REPL tests for Scala 3 using the Scala 3 REPL, rather than Ammonite (except for the tests where we do, in fact, test whether the Ammonite integration works as expected).

Dependencies

• Add a setting/API to run a code snippet/script in the REPL on startup scala/scala3#21242

Additional context

• NIT Extract REPL tests relying on Ammonite into dedicated traits #3209
• Ammonite 3.0.0 isn't published for Scala 3.3.3 com-lihaoyi/Ammonite#1563
• Deprecate object $ to avoid unsoundess com-lihaoyi/Ammonite#1395