Follow-up to #22612. Running `git status --short` in a loop during `make
-B -j gen` still showed intermediate states for several files. This PR
fixes the remaining ones.
The main issues:
- `generate.sh` ran `gofmt` and `goimports` in-place after moving files
into the source tree. Now it formats in a workdir first and only `mv`s
the final result.
- `protoc` targets wrote directly to the source tree. Wrapped with
`scripts/atomic_protoc.sh` which redirects output to a tmpdir.
- Several generators used hardcoded `/tmp/` paths. On systems where
`/tmp` is tmpfs, `mv` degrades to copy+delete. Switched to a
project-local `_gen/` directory (gitignored, same filesystem).
- `apidoc/.gen` and `cli/index.md` used `cp` for final output. Replaced
with `mv`.
- `manifest.json` was written twice (unformatted, then formatted). Now
`.gen` writes to a staging file and the manifest target does one
formatted atomic write.
- `biome_format.sh` silently skipped files in gitignored dirs. Added
`--vcs-enabled=false`.
Two helpers reduce the Makefile boilerplate: `scripts/atomic_protoc.sh`
(wraps protoc) and an `atomic_write` Make define
(stdout-to-temp-to-target pattern). `.PRECIOUS` now also covers `.pb.go`
and mock files.
Verification: `make -B -j gen` x3 with `git status` polling, no changes.
Refs #22612
Mathias Fredriksson