Just staying up to date

This is required for correctly loading the protobuf rules. It's
possible we could drop the version here to a lower version, as long as
that version supports the versions of bazel we support. I picked this
because it is the current version being used by bazel 8.0.0 (which is
defined in the .bazelversion). Users can override this in their project
anyways if they need an older one

vulkan_sdk_setup is the name of the method that configures it, but the
repo itself has the name vulkan_sdk

This was caught by enabling the bzlmod flag for CI. The GH action runs
`blaze test @llvm-project/...` but the target is tagged manual, so it's
excluded. The buildkite CI runs `bazel query | xargs bazel test` which
will include manual targets.

Switches to the config added in #164891

Fixes #55924

This is a simple translation of the current WORKSPACE file.

* External repos are replaced with `bazel_dep()`. The versions have been
bumped to newer versions.
* `maybe()` doesn't seem to be a thing, so I just removed that.
* Existing repos where we define our own BUILD file in third_party_build
have *not* been replaced due to compatibility issues. For example,
`nanobind_bazel` could replace the `nanobind` config we have, but
switching to that caused some build errors.
* For these existing repos, they have been specified as module
extensions

This should have no effect since `.bazelrc` defines `common
--enable_bzlmod=false --enable_workspace`

Tested locally: `bazel test --enable_bzlmod --noenable_workspace
--config=generic_clang @llvm-project//... //...`