Add explicit dependencies required for Bazel 9:
- rules_cc 0.2.16: provides cc_binary, cc_library, cc_test
- rules_java 9.0.3: provides java_* rules

Also update related dependencies:
- rules_go: 0.56.1 → 0.59.0 (compatibility with Bazel 9)
- gazelle: 0.40.0 → 0.47.0 (compatibility with rules_go 0.59.0)
- rules_nodejs: 6.2.0-codeql.1 → 6.7.3 (upstream version)

rules_python 1.x requires explicit toolchain setup and no longer
auto-registers toolchains. Register Python 3.12 toolchain to ensure
Python tools work correctly with Bazel 9.

Add +@rules_cc to --incompatible_autoload_externally to enable
graceful migration path for cc_* rule usages before all files
are updated with explicit imports.

Bazel 9 removes native.cc_* and CcInfo from global scope. Update:
- swift/rules.bzl: Add cc_binary, cc_library, CcInfo imports; use
  explicit cc_binary/cc_library instead of native.cc_*
- misc/bazel/cmake/cmake.bzl: Add CcInfo import for provider usage

Add explicit load statements for cc_binary, cc_library, and cc_test
from @rules_cc//cc:defs.bzl in:
- shared/cpp/BUILD.bazel
- swift/logging/BUILD.bazel
- misc/bazel/internal/zipmerge/BUILD.bazel

Add explicit load statements for java_library and java_test from
@rules_java//java:defs.bzl in:
- javascript/extractor/BUILD.bazel
- javascript/extractor/test/com/semmle/js/extractor/test/BUILD.bazel

Bazel 9 moves the C++ runfiles library from @bazel_tools to @rules_cc.
Update:
- zipmerge_test.cpp: Change include from tools/cpp/runfiles to
  rules_cc/cc/runfiles and update namespace accordingly
- BUILD.bazel: Update dependency from @bazel_tools//tools/cpp/runfiles
  to @rules_cc//cc/runfiles

Fix malformed JSON in metadata file - remove trailing comma after
last array element.