Remove automatic __init__.py generation (set incompatible_default_to_explicit_init_py to true)

The automatic generation of `__init__.py` files has been a source of odd, surprising, and incorrect behavior. e.g. it makes directories importable that shouldn't be importable. This is because it's logic is extremely simple: create an init.py file in every parent directory for a path that ends with .py or .so.

It's also expensive: it requires flattening the runfiles at analysis time.

Some of the venv site package work incidentally side-steps this because the way it creates symlinks "hides" some of the paths from the regular set of runfiles.

Addressing this is a bit more complicated because the incompatible_default_to_explicit_init_py lives in bazel, but the usage is in rules_python.

In any case, I think the todo list is:

1. [x] Add a rules_python flag to replace incompatible_default_to_explicit_init_py
2. [ ] Disable the behavior by default
3. [ ] Remove the dead code paths

Users can use `--flag_alias` to map (1) to the bazel builtin flag.

This is the rules_python side of https://github.com/bazelbuild/bazel/issues/7386

Start by tracing the rules_python usage of Bazel's incompatible_default_to_explicit_init_py flag and the runfiles analysis logic that automatically creates __init__.py files. Review the venv site package symlink behavior and the related Bazel issue. Done means the behavior is disabled by default and the resulting dead code paths are removed without breaking package handling.

Written by the indexing model from the issue text.