Use Xcode 16.4 in CI and fix non-bzlmod dependency issues (#1591)

Fixes:

```

buildkite-agent annotate --style=warning Your selected Xcode version 16.2 was not available on the machine.
--
  | Bazel CI automatically picked a fallback version: 26.0.


```

Also fixes issues in non-blzmod mode. We were resolving to dependency
versions that were newer than what was defined in `MODULE.bazel`, since
workspace mode does not upgrade deps for us it was failing to build due
to zlib issues fixed in newer protobuf versions. This updates the
versions to be set to what bzlmod is upgrading our deps to so we can
more accurately set the versions while in workspace mode

Fixes:

```
WARNING: For repository 'bazel_features', the root module requires module version [email protected], but got [email protected] in the resolved dependency graph. Please update the version in your MODULE.bazel or set --check_direct_dependencies=off
WARNING: For repository 'bazel_skylib', the root module requires module version [email protected], but got [email protected] in the resolved dependency graph. Please update the version in your MODULE.bazel or set --check_direct_dependencies=off
WARNING: For repository 'build_bazel_apple_support', the root module requires module version [email protected], but got [email protected] in the resolved dependency graph. Please update the version in your MODULE.bazel or set --check_direct_dependencies=off
WARNING: For repository 'platforms', the root module requires module version [email protected], but got [email protected] in the resolved dependency graph. Please update the version in your MODULE.bazel or set --check_direct_dependencies=off
WARNING: For repository 'com_google_protobuf', the root module requires module version [email protected], but got [email protected] in the resolved dependency graph. Please update the version in your MODULE.bazel or set --check_direct_dependencies=off
```

Author: luispadron

.bazelci/presubmit.yml

@@ -4,7 +4,7 @@ x_defaults:
   # it doesn't know about; so that is used to avoid repeating common subparts.
   mac_common: &mac_common
     platform: macos_arm64
-    xcode_version: "16.2"
+    xcode_version: "16.4"
     build_targets:
       - "//examples/..."
     test_targets:
@@ -63,7 +63,8 @@ tasks:
 
   macos_last_green:
     name: "Last Green Bazel"
-    bazel: last_green
+    # TODO: Use `last_green` when https://github.com/bazelbuild/bazel/pull/27330 merges
+    bazel: f2985041cb1170be4545049e1b4d25eea8a84660
     <<: *mac_common
 
   macos_latest_head_deps:
@@ -98,9 +99,8 @@ tasks:
 
   ubuntu2004_last_green:
     name: "Last Green Bazel"
-    # TODO: Use `last_green` when https://github.com/bazelbuild/bazel/issues/26962 is fixed
-    # bazel: last_green
-    bazel: 0522f8e58bf864005207eb8f09162d35ddd1f678
+    # TODO: Use `last_green` when https://github.com/bazelbuild/bazel/pull/27330 merges
+    bazel: f2985041cb1170be4545049e1b4d25eea8a84660
     shell_commands:
       - "echo --- Downloading and extracting Swift $SWIFT_VERSION to $SWIFT_HOME"
       - "mkdir $SWIFT_HOME"

MODULE.bazel

@@ -8,13 +8,13 @@ module(
     repo_name = "build_bazel_rules_swift",
 )
 
-bazel_dep(name = "bazel_features", version = "1.10.0")
-bazel_dep(name = "bazel_skylib", version = "1.3.0")
-bazel_dep(name = "apple_support", version = "1.21.0", repo_name = "build_bazel_apple_support")
+bazel_dep(name = "bazel_features", version = "1.30.0")
+bazel_dep(name = "bazel_skylib", version = "1.7.1")
+bazel_dep(name = "apple_support", version = "1.23.1", repo_name = "build_bazel_apple_support")
 bazel_dep(name = "rules_cc", version = "0.1.2")
 bazel_dep(name = "rules_shell", version = "0.3.0")
-bazel_dep(name = "platforms", version = "0.0.9")
-bazel_dep(name = "protobuf", version = "27.0", repo_name = "com_google_protobuf")
+bazel_dep(name = "platforms", version = "0.0.11")
+bazel_dep(name = "protobuf", version = "29.0", repo_name = "com_google_protobuf")
 bazel_dep(name = "nlohmann_json", version = "3.6.1", repo_name = "com_github_nlohmann_json")
 bazel_dep(
     name = "swift_argument_parser",

WORKSPACE

@@ -81,3 +81,11 @@ load("@rules_shell//shell:repositories.bzl", "rules_shell_dependencies", "rules_
 rules_shell_dependencies()
 
 rules_shell_toolchains()
+
+load("@com_google_protobuf//:protobuf_deps.bzl", "protobuf_deps")
+
+protobuf_deps()
+
+load("@rules_java//java:rules_java_deps.bzl", "rules_java_dependencies")
+
+rules_java_dependencies()

swift/repositories.bzl

@@ -48,17 +48,17 @@ def swift_rules_dependencies(include_bzlmod_ready_dependencies = True):
             http_archive,
             name = "bazel_skylib",
             urls = [
-                "https://github.com/bazelbuild/bazel-skylib/releases/download/1.3.0/bazel-skylib-1.3.0.tar.gz",
-                "https://mirror.bazel.build/github.com/bazelbuild/bazel-skylib/releases/download/1.3.0/bazel-skylib-1.3.0.tar.gz",
+                "https://github.com/bazelbuild/bazel-skylib/releases/download/1.7.1/bazel-skylib-1.7.1.tar.gz",
+                "https://mirror.bazel.build/github.com/bazelbuild/bazel-skylib/releases/download/1.7.1/bazel-skylib-1.7.1.tar.gz",
             ],
-            sha256 = "74d544d96f4a5bb630d465ca8bbcfe231e3594e5aae57e1edbf17a6eb3ca2506",
+            sha256 = "bc283cdfcd526a52c3201279cda4bc298652efa898b10b4db0837dc51652756f",
         )
 
         _maybe(
             http_archive,
             name = "build_bazel_apple_support",
-            url = "https://github.com/bazelbuild/apple_support/releases/download/1.21.0/apple_support.1.21.0.tar.gz",
-            sha256 = "293f5fe430787f3a995b2703440d27498523df119de00b84002deac9525bea55",
+            url = "https://github.com/bazelbuild/apple_support/releases/download/1.23.1/apple_support.1.23.1.tar.gz",
+            sha256 = "ee20cc5c0bab47065473c8033d462374dd38d172406ecc8de5c8f08487943f2f",
         )
 
         _maybe(
@@ -72,9 +72,19 @@ def swift_rules_dependencies(include_bzlmod_ready_dependencies = True):
         _maybe(
             http_archive,
             name = "com_google_protobuf",
-            urls = ["https://github.com/protocolbuffers/protobuf/releases/download/v27.0/protobuf-27.0.tar.gz"],
-            sha256 = "da288bf1daa6c04d03a9051781caa52aceb9163586bff9aa6cfb12f69b9395aa",
-            strip_prefix = "protobuf-27.0",
+            urls = ["https://github.com/protocolbuffers/protobuf/releases/download/v29.0/protobuf-29.0.tar.gz"],
+            sha256 = "10a0d58f39a1a909e95e00e8ba0b5b1dc64d02997f741151953a2b3659f6e78c",
+            strip_prefix = "protobuf-29.0",
+        )
+
+        # NOTE: this is required since `com_google_protobuf` depends on a bad 7.x version
+        # and WORKSAPCE mode does not upgrade the dependency correctly.
+        # This version matches that of the resolved rules_java version in `bazel mod graph`.
+        _maybe(
+            http_archive,
+            name = "rules_java",
+            url = "https://github.com/bazelbuild/rules_java/releases/download/8.14.0/rules_java-8.14.0.tar.gz",
+            sha256 = "bbe7d94360cc9ed4607ec5fd94995fd1ec41e84257020b6f09e64055281ecb12",
         )
 
         _maybe(
@@ -93,22 +103,40 @@ def swift_rules_dependencies(include_bzlmod_ready_dependencies = True):
         _maybe(
             http_archive,
             name = "bazel_features",
-            sha256 = "95fb3cfd11466b4cad6565e3647a76f89886d875556a4b827c021525cb2482bb",
-            strip_prefix = "bazel_features-1.10.0",
-            url = "https://github.com/bazel-contrib/bazel_features/releases/download/v1.10.0/bazel_features-v1.10.0.tar.gz",
+            sha256 = "a660027f5a87f13224ab54b8dc6e191693c554f2692fcca46e8e29ee7dabc43b",
+            strip_prefix = "bazel_features-1.30.0",
+            url = "https://github.com/bazel-contrib/bazel_features/releases/download/v1.30.0/bazel_features-v1.30.0.tar.gz",
         )
 
         _maybe(
             http_archive,
             name = "com_github_apple_swift_argument_parser",
-            urls = ["https://github.com/apple/swift-argument-parser/archive/refs/tags/1.3.0.tar.gz"],
-            sha256 = "e5010ff37b542807346927ba68b7f06365a53cf49d36a6df13cef50d86018204",
-            strip_prefix = "swift-argument-parser-1.3.0",
+            urls = ["https://github.com/apple/swift-argument-parser/archive/refs/tags/1.3.1.tar.gz"],
+            sha256 = "4d964f874b251abc280ee28f0f187de3c13a6122a9561524f66a10768ca2d837",
+            strip_prefix = "swift-argument-parser-1.3.1",
             build_file = Label(
                 "//third_party:com_github_apple_swift_argument_parser/BUILD.overlay",
             ),
         )
 
+        _maybe(
+            http_archive,
+            name = "rules_shell",
+            sha256 = "d8cd4a3a91fc1dc68d4c7d6b655f09def109f7186437e3f50a9b60ab436a0c53",
+            strip_prefix = "rules_shell-0.3.0",
+            url = "https://github.com/bazelbuild/rules_shell/releases/download/v0.3.0/rules_shell-v0.3.0.tar.gz",
+        )
+
+        _maybe(
+            http_archive,
+            name = "platforms",
+            urls = [
+                "https://mirror.bazel.build/github.com/bazelbuild/platforms/releases/download/0.0.11/platforms-0.0.11.tar.gz",
+                "https://github.com/bazelbuild/platforms/releases/download/0.0.11/platforms-0.0.11.tar.gz",
+            ],
+            sha256 = "29742e87275809b5e598dc2f04d86960cc7a55b3067d97221c9abbc9926bff0f",
+        )
+
     _maybe(
         http_archive,
         name = "com_github_apple_swift_protobuf",
@@ -252,14 +280,6 @@ def swift_rules_dependencies(include_bzlmod_ready_dependencies = True):
         sha256 = "9a54fc1674af6031125a9884480a1e31e1bcf48b8f558b3e8bcc6b6fcd6e8b61",
     )
 
-    _maybe(
-        http_archive,
-        name = "rules_shell",
-        sha256 = "d8cd4a3a91fc1dc68d4c7d6b655f09def109f7186437e3f50a9b60ab436a0c53",
-        strip_prefix = "rules_shell-0.3.0",
-        url = "https://github.com/bazelbuild/rules_shell/releases/download/v0.3.0/rules_shell-v0.3.0.tar.gz",
-    )
-
     _maybe(
         swift_autoconfiguration,
         name = "build_bazel_rules_swift_local_config",