fix(agentplugins): share one nativeconfig kernel across activate, verify, and identity

.github/workflows/core-fast.yml

@@ -63,9 +63,9 @@ jobs:
       - name: Report core coverage
         continue-on-error: true
         run: |
-          go list ./install/integrationctl/agentplugins/... \
+          (cd install/integrationctl/agentplugins && go list ./... \
             | grep -v '/adapters/clientdetect$' \
-            | xargs go test -count=1 -cover > core-cover.log 2>&1 || true
+            | xargs go test -count=1 -cover) > core-cover.log 2>&1 || true
           (cd cli/plugin-kit-ai && go test -count=1 -cover ./internal/agentpluginscli/... ./cmd/agentplugins/...) >> core-cover.log 2>&1 || true
           cat core-cover.log
           {

.github/workflows/coverage.yml

@@ -35,7 +35,11 @@ jobs:
           # incompatible with coverage instrumentation itself.
           go test -count=1 -timeout=20m -skip '^TestReleaseCompletionProcessStderr$' -covermode=atomic -coverprofile=coverage/cli.out ./cli/plugin-kit-ai/...
           go test -count=1 -timeout=20m -skip '^TestExecutableVersionProbeIsSanitizedAndIsolated$' -covermode=atomic -coverprofile=coverage/integrationctl.out ./install/integrationctl/...
-          go test -count=1 -timeout=20m -skip '^TestExecutableVersionProbeIsSanitizedAndIsolated$' -covermode=atomic -coverprofile=coverage/agentplugins.out ./install/integrationctl/agentplugins/...
+          # Nested module: do not use a parent-relative ./agentplugins/... glob.
+          # That pattern needs go.work; GOWORK=off fails loud instead of covering
+          # the child. cd keeps this job aligned with CodeQL / release / govulncheck.
+          agentplugins_cover="${PWD}/coverage/agentplugins.out"
+          (cd install/integrationctl/agentplugins && go test -count=1 -timeout=20m -skip '^TestExecutableVersionProbeIsSanitizedAndIsolated$' -covermode=atomic -coverprofile="$agentplugins_cover" ./...)
           go test -count=1 -timeout=20m -covermode=atomic -coverprofile=coverage/plugininstall.out ./install/plugininstall/...
           go test -count=1 -timeout=20m -covermode=atomic -coverprofile=coverage/sdk.out ./sdk/...
 

Makefile

@@ -47,7 +47,8 @@ lint-baseline-check:
 test-core:
 	# adapters/pathpolicy is outside the agentplugins tree but holds the only
 	# ports.PathPolicy implementation, so the fast gate has to run it too.
-	$(CORE_TEST_GIT_ENV) go test -count=1 -timeout=$(CORE_TEST_TIMEOUT) ./install/integrationctl/agentplugins/... ./install/integrationctl/adapters/pathpolicy/...
+	cd install/integrationctl && $(CORE_TEST_GIT_ENV) go test -count=1 -timeout=$(CORE_TEST_TIMEOUT) ./adapters/pathpolicy/...
+	cd install/integrationctl/agentplugins && $(CORE_TEST_GIT_ENV) go test -count=1 -timeout=$(CORE_TEST_TIMEOUT) ./...
 	cd cli/plugin-kit-ai && $(CORE_TEST_GIT_ENV) go test -count=1 -timeout=$(CORE_TEST_TIMEOUT) ./internal/agentpluginscli/... ./cmd/agentplugins/...
 
 test:
@@ -57,7 +58,7 @@ test-required:
 	go test -count=1 -timeout=$(REQUIRED_TEST_TIMEOUT) ./...
 	go test -count=1 -timeout=$(REQUIRED_TEST_TIMEOUT) ./cli/plugin-kit-ai/...
 	go test -count=1 -timeout=$(REQUIRED_TEST_TIMEOUT) ./install/integrationctl/...
-	go test -count=1 -timeout=$(REQUIRED_TEST_TIMEOUT) ./install/integrationctl/agentplugins/...
+	cd install/integrationctl/agentplugins && go test -count=1 -timeout=$(REQUIRED_TEST_TIMEOUT) ./...
 	go test -count=1 -timeout=$(REQUIRED_TEST_TIMEOUT) ./install/plugininstall/...
 	go test -count=1 -timeout=$(REQUIRED_TEST_TIMEOUT) ./sdk/...
 	cd npm/agentplugins && npm test && npm pack --dry-run --ignore-scripts

cli/plugin-kit-ai/cmd/agentplugins/compose.go

@@ -16,6 +16,7 @@ import (
 	"github.com/777genius/plugin-kit-ai/install/integrationctl/agentplugins/adapters/directoryv1"
 	"github.com/777genius/plugin-kit-ai/install/integrationctl/agentplugins/adapters/discoveryv1"
 	"github.com/777genius/plugin-kit-ai/install/integrationctl/agentplugins/adapters/loader"
+	"github.com/777genius/plugin-kit-ai/install/integrationctl/agentplugins/adapters/nativeconfig"
 	"github.com/777genius/plugin-kit-ai/install/integrationctl/agentplugins/adapters/processlock"
 	"github.com/777genius/plugin-kit-ai/install/integrationctl/agentplugins/adapters/securityscan"
 	"github.com/777genius/plugin-kit-ai/install/integrationctl/agentplugins/adapters/securityv1"
@@ -68,9 +69,10 @@ func newAgentpluginsCLIApp(home, dataRoot string, directoryClient *directoryv1.C
 	mutationLock := processlock.Lock{Path: filepath.Join(dataRoot, "mutation.lock")}
 	clientRegistry := clientregistry.Default()
 	paths := pathpolicy.Policy{}
+	nativeKernel := nativeconfig.New()
 	stager := newManagedStager(clientRegistry, paths)
 	planner := clientplanner.Planner{ManagedRoot: filepath.Join(dataRoot, "managed"), Paths: paths, Registry: clientRegistry}
-	lifecycle := newAgentpluginsLifecycle(dataRoot, v2Store, paths, clientRegistry, stager, runner, planner, directoryManager, mutationLock)
+	lifecycle := newAgentpluginsLifecycle(dataRoot, v2Store, paths, clientRegistry, stager, runner, planner, directoryManager, mutationLock, nativeKernel)
 	return assembleAgentpluginsApp(home, dataRoot, v2Store, mutationLock, lifecycle, directoryClient, discoveryClient, securityClient, packageLoader, clientRegistry, planner)
 }
 
@@ -84,12 +86,12 @@ func newManagedStager(clientRegistry *clients.Registry, paths pathpolicy.Policy)
 	return stager
 }
 
-func newAgentpluginsLifecycle(dataRoot string, v2Store statev2.Store, paths pathpolicy.Policy, clientRegistry *clients.Registry, stager providers.Stager, runner processadapter.OS, planner clientplanner.Planner, directoryManager dirswap.Manager, mutationLock processlock.Lock) usecase.Service {
+func newAgentpluginsLifecycle(dataRoot string, v2Store statev2.Store, paths pathpolicy.Policy, clientRegistry *clients.Registry, stager providers.Stager, runner processadapter.OS, planner clientplanner.Planner, directoryManager dirswap.Manager, mutationLock processlock.Lock, nativeKernel nativeconfig.Kernel) usecase.Service {
 	return usecase.Service{
 		StateStore: v2Store, Paths: paths, Planner: planner, Targets: planner, Stager: stager,
-		Activator: providers.Activator{Runner: runner, Registry: clientRegistry},
+		Activator: providers.Activator{Runner: runner, Registry: clientRegistry, NativeConfig: &nativeKernel},
 		Lock:      mutationLock, Kernel: transaction.Kernel{StateStore: v2Store, Directory: directoryManager},
-		NativeObserver: providers.NativeIdentityObserver{Stager: stager, Runner: runner, Registry: clientRegistry},
+		NativeObserver: providers.NativeIdentityObserver{Stager: stager, Runner: runner, Registry: clientRegistry, NativeConfig: &nativeKernel},
 		PluginData:     providers.PluginDataManager{Base: filepath.Join(dataRoot, "plugin-data")},
 	}
 }

docs/ARCHITECTURE.md

@@ -44,7 +44,7 @@ point inward.
 | Client adapters | `agentplugins/clients/<id>` | the client contract, `clients/shared`, `domain`, `ports` | yes, `clients-no-upward`, `clients-no-concrete-clients` |
 | Adapters | `agentplugins/{adapters,providers,planner}` | the layers above, never `clients/all` | partly, `libraries-take-an-injected-registry` |
 | CLI | `agentpluginscli` | the public facades of the layers above, never providers or pathpolicy | yes, `cli-no-core-internals` |
-| Composition root | `cmd/agentplugins` | everything, and nothing imports it | yes: it is the only production importer of `clients/all` |
+| Composition root | `cmd/agentplugins`, `cmd/plugin-kit-ai` | everything, and nothing imports them | yes: they are the production importers of `clients/all` |
 
 The "Enforced today" column is deliberate: the middle column is the target, and
 the left-hand rules are checked by `depguard` in `.golangci.yml`. Domain, ports,
@@ -71,10 +71,11 @@ adapter into any binary that imports a generic package and would put the registr
 outside the composition root's control. `libraries-take-an-injected-registry`
 holds the other side of that line: `providers`, `planner` and
 `adapters/clientdetect` may not import `clients/all` outside their tests, so the
-assembled registry reaches them only as an argument. `cmd/agentplugins` is the
-one place that builds it. The CLI receives `Planner`, `Targets` and `Registry`
-from that root; it does not construct `planner.Planner{}`. Detection is
-request-scoped: `domain.PlanRequest.Detected` is the map `Planner.Plan` reads.
+assembled registry reaches them only as an argument. `cmd/agentplugins` and
+`cmd/plugin-kit-ai` are the production places that build it. The installer CLI
+receives `Planner`, `Targets` and `Registry` from that root; it does not
+construct `planner.Planner{}`. Detection is request-scoped:
+`domain.PlanRequest.Detected` is the map `Planner.Plan` reads.
 
 `cli-no-core-internals` keeps `agentpluginscli` off `providers` and
 `pathpolicy`. The CLI may still import the thin public planner facade

docs/adr/0007-client-adapter-contract-and-registry.md

@@ -22,9 +22,10 @@ compensation, not a substitute for a module boundary.
 ## Decision
 
 Client-specific behavior lives in `install/integrationctl/agentplugins/clients/<id>`.
-The composition root (`cli/plugin-kit-ai/cmd/agentplugins`) is the only
-production package that imports `clients/all`. Generic packages receive a
-`clients.Registry` and fail closed when it is nil.
+The production composition roots that import `clients/all` are
+`cli/plugin-kit-ai/cmd/agentplugins` (installer CLI) and
+`cli/plugin-kit-ai/cmd/plugin-kit-ai` (authoring CLI). Generic packages receive
+a `clients.Registry` and fail closed when it is nil.
 
 Invariants:
 

docs/plans/installer-core-clean-architecture-plan.md

@@ -555,7 +555,7 @@ issues:
 
 Один режим на всё не работает: `new-from-*` фильтрует по изменённым строкам, а `funlen`/`gocyclo`/`file-length-limit` репортят на строке объявления функции/файла — добавление 40 строк в середину старой 200-строчной функции такой фильтр не поймает. Поэтому:
 
-- **Прогон A** — корректность и стиль, только изменённые строки: все линтеры, кроме size/arch. CI: `only-new-issues: true` (на PR — патч через GitHub API; на push — `new-from-rev=<before>`). Локально: `golangci-lint run --new-from-merge-base=$(BASE)`; в checkout нужен `fetch-depth: 0`.
+- **Прогон A** — корректность и стиль, только изменённые строки: все линтеры, кроме size/arch. CI и локально: `golangci-lint run --new-from-merge-base=$(LINT_BASE)`. `LINT_BASE` на PR — `origin/<base>` (для stacked part-PR это architecture, для `#288` — `main`). `golangci-lint-action` `only-new-issues` здесь нельзя: reusable `workflow_call` не несёт `github.event.pull_request`, а GitHub Files API отдаёт 406 на diff > 300 файлов и молча падает в полный прогон. В checkout нужен `fetch-depth: 0` и явный `git fetch` базовой ветки.
 - **Прогон B** — size/arch-гейт, полные файлы, всегда: `golangci-lint run --enable-only=revive,funlen,gocyclo,gocognit,dupl,depguard`. Легаси-нарушения размера покрыты baseline-исключениями (сгенерированы этим же прогоном в Part 0a); всё остальное строго: новый файл > 500 строк кода, новая функция > 60/40, рост сложности в файле вне baseline, любой запрещённый импорт — красный. `depguard` в full-file режиме — граница держится всегда, а не только на изменённых строках.
 - **Baseline shrink-only**: `scripts/check-lint-baseline.sh <base-ref>` извлекает блок `BEGIN/END LEGACY SIZE BASELINE` из `.golangci.yml` в HEAD и из `git show <base-ref>:.golangci.yml`, `comm -13` → любые добавленные `- path:` = ошибка. Файл из скоупа выходит из baseline в той части, которая его режет (критерий приёмки части). В Part 11 блок содержит только файлы вне скоупа (§11).
 
@@ -565,21 +565,30 @@ issues:
 name: Lint
 on:
   workflow_call:
+    inputs:
+      lint-base: { type: string, default: origin/main }
 jobs:
   lint:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        module: [".", "cli/plugin-kit-ai", "install/integrationctl"]
+        include:
+          - { name: root, module: "" }
+          - { name: cli/plugin-kit-ai, module: cli/plugin-kit-ai }
+          - { name: install/integrationctl, module: install/integrationctl }
+          - { name: install/integrationctl/agentplugins, module: install/integrationctl/agentplugins }
     steps:
       - uses: actions/checkout@<sha>   # v7.0.1, пин по SHA как остальные actions в репо
         with: { persist-credentials: false, fetch-depth: 0 }
+      - name: Fetch lint base
+        env: { LINT_BASE: ${{ inputs.lint-base }} }
+        run: git fetch --no-tags origin "${LINT_BASE#origin/}:refs/remotes/origin/${LINT_BASE#origin/}"
       - uses: actions/setup-go@<sha>    # v7.0.0
         with: { go-version: "1.25.13", cache: false }
       - name: Lint changed lines (correctness, style)
         uses: golangci/golangci-lint-action@<sha>   # v9.3.0
-        with: { version: v2.13.2, working-directory: ${{ matrix.module }}, only-new-issues: true }
+        with: { version: v2.13.2, working-directory: ${{ matrix.module }}, only-new-issues: false, args: --new-from-merge-base=${{ inputs.lint-base }} }
       - name: Size and architecture gate (full files)
         uses: golangci/golangci-lint-action@<sha>   # v9.3.0
         with:
@@ -588,13 +597,14 @@ jobs:
           only-new-issues: false
           args: --enable-only=revive,funlen,gocyclo,gocognit,dupl,depguard
       - name: Baseline is shrink-only
-        if: matrix.module == '.'
-        run: bash scripts/check-lint-baseline.sh "origin/${{ github.base_ref || 'main' }}"
+        if: matrix.name == 'root'
+        env: { LINT_BASE: ${{ inputs.lint-base }} }
+        run: bash scripts/check-lint-baseline.sh "$LINT_BASE"
 ```
 
 Матрица покрывает модули с кодом ядра (включая nested `install/integrationctl/agentplugins`); `install/plugininstall` и `sdk` из `go.work` линтом не покрываются (не меняются планом), но покрываются `go vet` в `core-fast` (§10).
 
-`ci.yml`: `jobs.lint: uses: ./.github/workflows/lint.yml` параллельно с `test`. Почему отдельный job, а не шаг в `test`: `test` — критический путь 9-27 мин; lint в трёх параллельных матричных job ожидаемо 3-5 мин и не удлиняет путь; при этом он в том же workflow «Required», т.е. входит в required-гейт.
+`ci.yml` / `core-fast.yml` передают `lint-base: origin/${{ github.base_ref || 'main' }}` — caller видит `github.base_ref`, called workflow на `workflow_call` его не имеет. Почему отдельный job, а не шаг в `test`: `test` — критический путь 9-27 мин; lint в четырёх параллельных матричных job ожидаемо 3-5 мин и не удлиняет путь; при этом он в том же workflow «Required», т.е. входит в required-гейт.
 
 Версии: golangci-lint v2.13.2 (релиз 2026-08-27) и golangci-lint-action v9.3.0 (2026-06-29) — последние стабильные по GitHub Releases на дату плана (VERIFIED). Локально нужен апгрейд с v1.64.8 (`brew upgrade golangci-lint`): v1 не читает `version: "2"` и не содержит правило `file-length-limit`.
 
@@ -979,7 +989,7 @@ Wall 5-7 мин и для `main`. Полезно, но меняет общий C
 - Код конкурента AgentBridge (оценки взяты из аудита пользователя).
 - Длительность CLI-тестов и root `./...` в CI по отдельности (замерено только локально: `ap/...` = 62.6 с, CLI-пакет = 56 с).
 - Точный состав `gocritic disabled-checks`/`gosec excludes` и порог `dupl` — по первому прогону в Part 0a.
-- Поведение `golangci-lint-action only-new-issues` для `push`-событий (`new-from-rev=before`) — по документации action; проверить на первом push в базовую ветку.
+- Поведение `--new-from-merge-base` на `push` в `main` (`lint-base` = `origin/main` = HEAD): прогон A вырождается в no-op, size/arch всё равно полный. Для architecture-push сравнение с `origin/main` — нужный гейт для `#288`.
 - Поведение `depguard` при `relative-path-mode: gitroot` для glob-паттернов `files:` — проверить на негативных тестах Part 0a (§6.7, п.3).
 - Аргументы `revive file-length-limit` прочитаны в исходниках `mgechev/revive` (`rule/file_length_limit.go`, `rule/utils.go`, `internal/config/config.go`) на ветке `master`, а не на теге, вшитом в golangci-lint v2.13.2 — теоретически они могли отличаться в момент вендоринга. Негативный тест §6.7 п.3 закрывает это эмпирически на первом прогоне.
 - Точное число мест конструирования `Service{}`/`Planner{}`: подсчёты разными способами дают 23/32 (grep по строкам на HEAD) против 23/39 (подсчёт критика). Планируем по верхней границе ≈62; точное число выяснится при первой компиляции после введения fail-fast.

install/integrationctl/agentplugins/adapters/nativeconfig/kernel.go

@@ -31,13 +31,23 @@ func (kernel Kernel) Apply(req Request) (Receipt, error) {
 	return receipts[0], err
 }
 
+// RequireFileIO reports that this kernel can Inspect and Apply. A zero Kernel
+// has no FileIO and must not be used as a hide-default on skill-only native
+// paths that never call ApplyBatch.
+func (kernel Kernel) RequireFileIO() error {
+	if kernel.files == nil {
+		return fmt.Errorf("native config file IO is required")
+	}
+	return nil
+}
+
 // ApplyBatch validates and renders related MCP entry mutations into one atomic
 // replacement. The batch is all-or-none for cooperating agentplugins writers.
 // See conditionalFileIO for the unavoidable portable race with clients that do
 // not honor the same locks.
 func (kernel Kernel) ApplyBatch(requests []Request) (receipts []Receipt, err error) {
-	if kernel.files == nil {
-		return nil, fmt.Errorf("native config file IO is required")
+	if err := kernel.RequireFileIO(); err != nil {
+		return nil, err
 	}
 	if len(requests) == 0 {
 		return nil, nil
@@ -178,8 +188,8 @@ func (kernel Kernel) ApplyBatch(requests []Request) (receipts []Receipt, err err
 
 // Inspect performs a strict read-only ownership check for one native entry.
 func (kernel Kernel) Inspect(paths Paths, codec Codec, name string, owned *Receipt) (present bool, exactlyOwned bool, err error) {
-	if kernel.files == nil {
-		return false, false, fmt.Errorf("native config file IO is required")
+	if err := kernel.RequireFileIO(); err != nil {
+		return false, false, err
 	}
 	if strings.TrimSpace(name) == "" {
 		return false, false, fmt.Errorf("MCP entry name is required")

install/integrationctl/agentplugins/adapters/nativeconfig/kernel_test.go

@@ -12,6 +12,16 @@ import (
 	"time"
 )
 
+func TestRequireFileIORejectsZeroKernel(t *testing.T) {
+	t.Parallel()
+	if err := (Kernel{}).RequireFileIO(); err == nil || !strings.Contains(err.Error(), "native config file IO is required") {
+		t.Fatalf("zero Kernel was not fail-closed: %v", err)
+	}
+	if err := New().RequireFileIO(); err != nil {
+		t.Fatalf("production Kernel rejected FileIO: %v", err)
+	}
+}
+
 func TestMCPServersAddPreservesUnrelatedConfigAndResolvesExplicitPaths(t *testing.T) {
 	root := t.TempDir()
 	path := filepath.Join(root, "client.json")