Add CodeGeneratorRequestWriter from Base; fix plugins to work with Gradle cache; fix ArtifactMetaPlugin working directory

.agents/tasks/archive/938-move-codegen-request-writer.md

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+---
+slug: 938-move-codegen-request-writer
+branch: claude/busy-dirac-wwflbm
+owner: claude
+status: in-progress
+started: 2026-06-10
+---
+
+## Goal
+
+`CodeGeneratorRequestWriter` lives in the `tool-base` module under
+`io.spine.tools.code.proto`, with its spec, and the build is green.
+This is the receiving half of
+[base-libraries#938](https://github.com/SpineEventEngine/base-libraries/issues/938).
+
+## Context
+
+- The class is protoc-plugin tooling; its only consumers are the protoc-plugin
+  entry points of the Compiler and ProtoTap. Both already depend on ToolBase.
+- Repackaged from `io.spine.code.proto` to `io.spine.tools.code.proto` to avoid
+  a split package across artifacts (see the issue discussion).
+- `replaceExtension` is still consumed from `io.spine.io` (`base`); it moves to
+  ToolBase later under base-libraries#939.
+- The removal half happens in `base-libraries` on the same-named branch.
+
+## Plan
+
+- [x] Add `CodeGeneratorRequestWriter.kt` to
+  `tool-base/src/main/kotlin/io/spine/tools/code/proto/`.
+- [x] Add `CodeGeneratorRequestWriterSpec.kt` (with a local `constructRequest`
+  helper) to `tool-base/src/test/kotlin/io/spine/tools/code/proto/`.
+- [x] Bump version `2.0.0-SNAPSHOT.398` -> `2.0.0-SNAPSHOT.399`.
+- [ ] `./gradlew build` green; commit regenerated dependency reports if any.
+  - Blocked in the sandbox: all Spine artifact repositories return 403 for
+    the buildscript dependency `io.spine.tools:protobuf-setup-plugins`, so
+    no Gradle build can run here at all. Verification is delegated to PR CI.
+  - Local mitigations: the moved sources are unchanged from `base` (which
+    built and passed tests) except the package line, and every consumed API
+    (`replaceExtension`, `decodeBase64`, `toBase64Encoded`,
+    `extensionRegistry`, `KClass.parse`, `toJson`) was verified present in
+    `base` at the pinned version `2.0.0-SNAPSHOT.404`.
+- [x] Push and open a draft PR.
+
+## Log
+
+- 2026-06-10 — drafted; executing autonomously per issue #938.
+- 2026-06-10 — code added and version bumped; sandbox cannot resolve Spine
+  snapshot artifacts (403 on all repos), so the build runs on PR CI instead.

.agents/tasks/archive/fix-build-cache-support.md

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+---
+slug: fix-build-cache-support
+branch: claude/busy-dirac-wwflbm
+owner: claude
+status: in-review
+started: 2026-06-10
+---
+
+## Goal
+
+Builds of projects using the `io.spine.generated-sources` and
+`io.spine.descriptor-set-file` plugins succeed with `org.gradle.caching=true`:
+after `./gradlew clean build`, the copied generated code under
+`$projectDir/generated/<sourceSet>` and the `desc.ref` file are present even
+when `generateProto` is restored from the Gradle build cache.
+
+## Context
+
+With the build cache on, `clean build` fails in the `classic-codegen` module
+(reproduced locally): `compileKotlin` reports `Unresolved reference 'Classpath'`
+because no generated code is present.
+
+Root cause — same pattern as SpineEventEngine/compiler#67. Both plugins in
+`protobuf-setup-plugins` do work in `doLast` of the cacheable
+`GenerateProtoTask` without declaring outputs:
+
+- `GeneratedSourcePlugin` copies protoc output into
+  `$projectDir/generated/<sourceSet>/` (undeclared — the build-breaker:
+  `clean` deletes `generated/`, the task is restored `FROM-CACHE`, the
+  `doLast` copy never runs, compilation fails).
+- `DescriptorSetFilePlugin` writes `desc.ref` next to the descriptor set file
+  (undeclared — missing from resources/JARs after a cache restore).
+
+The descriptor set file itself is already a declared output of
+`GenerateProtoTask` (verified for protobuf-gradle-plugin 0.10.0 in
+compiler#67), so only `desc.ref` needs declaring.
+
+This repository's own build applies the *published*
+`protobuf-setup-plugins:2.0.0-SNAPSHOT.381` (dogfooding via the root
+buildscript classpath), so `org.gradle.caching` stays disabled in
+`gradle.properties` until a fixed version is published and the dogfooded
+`ToolBase.version` is bumped (decision confirmed by the user).
+
+Known limitation (out of scope): in repos where the Spine Compiler launch
+task also writes into `generated/<sourceSet>` (e.g. `validation`), the
+overlapping outputs degrade cacheability of the codegen tasks; correctness
+is preserved because Gradle re-executes instead of restoring.
+
+## Plan
+
+- [x] Diagnose and reproduce on `classic-codegen` (`build` → `clean` →
+      `build` with `--build-cache`).
+- [x] `GeneratedSourcePlugin`: declare `$projectDir/generated/<sourceSet>`
+      as an output of `GenerateProtoTask`.
+- [x] `DescriptorSetFilePlugin`: declare `desc.ref`
+      (`DescriptorSetReferenceFile.NAME`) as an output.
+- [x] `gradle.properties`: keep `org.gradle.caching` commented out; explain
+      the dogfooding gate.
+- [x] Integration tests in `protobuf-setup-plugins` (TestKit, per existing
+      spec style): `build` → `clean` → `build` with the cache ON (assert
+      `generateProto` is `FROM_CACHE`, generated sources + `desc.ref`
+      restored, compilation of code referencing a generated class succeeds)
+      and with the cache OFF (assert re-execution works as before).
+- [x] Verify: new tests fail without the fix, pass with it; module build
+      green.
+
+## Log
+
+- 2026-06-10 — Investigated; reproduced on `classic-codegen` with the
+  dogfooded `.381` plugins; user chose to keep `org.gradle.caching` disabled
+  until dogfooding catches up.
+- 2026-06-10 — The new integration test exposed a second gap: in a pure-Java
+  project `compileJava` does not depend on `generateProto` because
+  `configureSourceSetDirs()` severs the dependency carried by the protoc
+  output dirs and adds the `generated/` dirs as plain `File`s. (Masked in
+  Spine repos by the Kotlin compile dependency from `setupKotlinCompile()`.)
+  Fixed by adding the dirs via `project.files(dir).builtBy(task)`.
+- 2026-06-10 — Verified: with the output declarations temporarily removed,
+  the cache-on test fails and the cache-off test passes; with the fix both
+  pass. `:protobuf-setup-plugins:build` and `dokkaGenerate` are green
+  (11 test suites, 0 failures).
+- 2026-06-10 — Reviewed by `spine-code-review` and `kotlin-engineer` agents:
+  both approve. Applied follow-ups: `internal` on `BuildCacheSpec`,
+  explicit `this@configureSourceSetDirs` in `builtBy`, fixed stale
+  `copyGeneratedFiles` KDoc. Final build: 22 tests, 0 failures.