(fix)build: disable proto rule generation, rely on checked-in .pb.go for go-code compatibility

[roychying]

Why?

We want the smoothest DX for consuming the OSS submitqueue repo in go-code. Today go-code's go_repository uses build_file_generation = "on", so its Gazelle regenerates BUILD files for the vendored repo. This causes conflicts and mismatches, and every version bump risks new patching. The end goal is build_file_generation = "off" so go-code uses the OSS BUILD files directly - but that requires OSS to be buildable out-of-the-box under go-code's toolchain, which it isn't today.

The root issue is that OSS carries proto types twice: as checked-in .pb.go in protopb/, and as Bazel-generated code via go_proto_library in proto/. Removing the Bazel proto rules in favor of the checked-in .pb.go fixes several things at once:

• Unblocks go-code's build. The proto_library rules trigger a transitive load of @protobuf//, which calls native.java_proto_library - removed in go-code's Bazel 8.5.1. Removing them removes the breakage.
• Eliminates duplicate proto definitions. The two generation paths share the same importpath, which caused the duplicate-importpath ambiguity and forced the gazelle:resolve workarounds. Collapsing to a single source removes that whole class of conflict.
• Serves non-Bazel consumers. The Bazel-generated code only exists inside a Bazel build graph. Anyone consuming submitqueue via plain go build/go get (including OSS users) can only use the checked-in .pb.go, so that path must work regardless. The Bazel proto rules are a redundant second path that serves no one the checked-in files don't already serve.

What?

Disable Gazelle proto rule generation and remove all proto compilation rules, relying solely on checked-in .pb.go files.

• Add # gazelle:proto disable_global to prevent Gazelle from regenerating proto rules on future make gazelle runs
• Remove the gazelle:resolve directives that are no longer needed
• Remove proto_library, go_proto_library, and alias go_library rules
• Keep exports_files for make proto codegen (tool/proto/BUILD.bazel)

Test Plan

• make build - pass
• make test - 65/65 unit tests pass (integration/e2e tests fail due to Docker dependency, pre-existing)
• bazel build //tool/proto:generated - proto codegen still works
• make gazelle - zero warnings, no duplicate-importpath ambiguity
• Validated in go-code with --override_repository pointing at this branch: all 71 targets build, all 20 tests pass across stovepipe, submitqueue/gateway, and submitqueue/orchestrator

Issue

[CLAassistant]

Thank you for your submission! We really appreciate it. Like many open source projects, we ask that you sign our Contributor License Agreement before we can accept your contribution.

---

chenghan.ying seems not to be a GitHub user. You need a GitHub account to be able to sign the CLA. If you have already a GitHub account, please add the email address used for this commit to your account.
_{You have signed the CLA already but the status is still pending? Let us recheck it.}