We change the bootstrap scripts so that they invoke build/bin/sage-package directly instead of going through the SAGE_ROOT/sage script.

This is faster and also more robust because it separates build phases better by eliminating the (unnecessary) use of configure-generated files such as src/bin/sage-src-env-config.

We also move the generation of src/doc/en/reference/repl/options.txt (by calling sage -advanced) from bootstrap time to src/doc/Makefile. The information displayed there depends on what packages are installed, so running it at bootstrap time was not correct.

Depends on #33740

CC: @jhpalmieri @tobiasdiez @orlitzky @dimpase @kiwifb

Component: scripts

Author: Matthias Koeppe

Branch/Commit: 67c8238

Reviewer: John Palmieri, François Bissey

Issue created by migration from https://trac.sagemath.org/ticket/33852