[codex] Split backend control-plane QoL slice (#4700)

## Thinking Path

> - Paperclip is the control plane for autonomous AI companies, so
backend task ownership, recovery, review visibility, and company-scoped
limits need to stay enforceable without UI-only coupling.
> - Closed PR #4692 bundled those backend changes with UI workflow,
docs, skills, workflow, and lockfile churn.
> - PAP-2694 asks for a clean backend/control-plane slice from that
closed branch.
> - This branch starts from current `master` and mines only the `cli`,
`packages/db`, `packages/shared`, and `server` contracts/tests needed
for the backend behavior.
> - It explicitly excludes UI workflow/performance work,
`.github/workflows/pr.yml`, `pnpm-lock.yaml`, docs, skills,
package-script, adapter UI build-config, and perf fixture script
changes; the only UI files are fixture/test updates required by the
tightened shared `Company` contract.
> - The benefit is a smaller reviewable PR that preserves the
control-plane fixes while staying under Greptile s 100-file review
limit.

## What Changed

- Added company-scoped attachment-size limits through DB
schema/migrations, shared company portability contracts, CLI
import/export coverage, and server attachment upload enforcement.
- Added productivity review service/API behavior for no-comment streak,
long-active, and high-churn review issues, including request-depth
clamping and issue summary exposure.
- Hardened issue ownership and recovery/control-plane paths: peer-agent
mutation denial, issue tree pause/resume behavior, stranded recovery
origins, and related activity/test coverage.
- Preserved related backend contract updates for routine timestamp
variables and managed agent instruction bundles because they live in
shared/server contracts from the source branch.
- Addressed Greptile feedback by making `Company.attachmentMaxBytes`
non-optional, simplifying review request-depth clamping, fixing the
migration final newline, and enforcing the process-level attachment cap
as the final ceiling for uploads.
- Added minimal company fixtures needed for repo-wide typecheck/build
and kept the PR to 66 changed files with forbidden/non-slice paths
excluded.

## Verification

- `pnpm install --frozen-lockfile`
- `git diff --check origin/master..HEAD`
- `git diff --name-only origin/master..HEAD | wc -l` -> 66 files
- `git diff --name-only origin/master..HEAD -- .github/workflows/pr.yml
pnpm-lock.yaml package.json doc skills .agents scripts
packages/adapters` -> no output
- `pnpm exec vitest run --config vitest.config.ts
packages/shared/src/validators/issue.test.ts
packages/shared/src/routine-variables.test.ts
packages/shared/src/adapter-types.test.ts
cli/src/__tests__/company-import-export-e2e.test.ts
cli/src/__tests__/company.test.ts
server/src/__tests__/productivity-review-service.test.ts
server/src/__tests__/issue-tree-control-service.test.ts
server/src/__tests__/issue-tree-control-routes.test.ts
server/src/__tests__/issue-agent-mutation-ownership-routes.test.ts
server/src/__tests__/issue-attachment-routes.test.ts
server/src/__tests__/heartbeat-process-recovery.test.ts
server/src/__tests__/issues-service.test.ts` -> 12 files, 147 tests
passed
- `pnpm exec vitest run --config vitest.config.ts
cli/src/__tests__/company-delete.test.ts
cli/src/__tests__/company-import-export-e2e.test.ts
server/src/__tests__/productivity-review-service.test.ts` -> 3 files, 18
tests passed
- `pnpm exec vitest run --config vitest.config.ts
server/src/__tests__/issue-attachment-routes.test.ts` -> 1 file, 6 tests
passed
- `pnpm --filter @paperclipai/db typecheck && pnpm --filter
@paperclipai/shared typecheck && pnpm --filter @paperclipai/server
typecheck && pnpm --filter paperclipai typecheck`
- `pnpm --filter @paperclipai/server typecheck`
- `pnpm --filter @paperclipai/ui typecheck && pnpm --filter
@paperclipai/ui build`

## Risks

- Includes migrations `0073_shiny_salo.sql` and
`0074_striped_genesis.sql`; merge ordering matters if another PR adds
migrations first.
- This is intentionally backend-only apart from fixture/test updates
forced by shared type correctness; UI affordances from PR #4692 are not
present here and should land in separate UI slices.
- The worktree install emitted plugin SDK bin-link warnings for unbuilt
plugin packages, but the targeted tests and package typechecks completed
successfully.

> For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and
discuss it in `#dev` before opening the PR. Feature PRs that overlap
with planned core work may need to be redirected; check the roadmap
first. See `CONTRIBUTING.md`.

## Model Used

- OpenAI Codex, GPT-5 coding agent, tool-enabled terminal/GitHub
workflow. Exact runtime context window was not exposed by the harness.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>

server/src/__tests__/agent-skills-routes.test.ts

@@ -481,8 +481,11 @@ describe.sequential("agent skill routes", () => {
         name: "QA Agent",
         role: "engineer",
         adapterType: "claude_local",
-        adapterConfig: {
-          promptTemplate: "You are QA.",
+        adapterConfig: {},
+        instructionsBundle: {
+          files: {
+            "AGENTS.md": "You are QA.",
+          },
         },
       }));
 
@@ -504,6 +507,26 @@ describe.sequential("agent skill routes", () => {
     });
   });
 
+  it("rejects legacy prompt templates for directly created local agents", async () => {
+    const res = await requestApp(await createApp(), (baseUrl) => request(baseUrl)
+      .post("/api/companies/company-1/agents")
+      .send({
+        name: "QA Agent",
+        role: "engineer",
+        adapterType: "claude_local",
+        adapterConfig: {
+          instructionsFilePath: "/tmp/existing/AGENTS.md",
+          promptTemplate: "You are QA.",
+          bootstrapPromptTemplate: "Bootstrap QA.",
+        },
+      }));
+
+    expect(res.status, JSON.stringify(res.body)).toBe(422);
+    expect(res.body.error).toContain("New agents must use instructionsBundle/AGENTS.md");
+    expect(mockAgentService.create).not.toHaveBeenCalled();
+    expect(mockAgentInstructionsService.materializeManagedBundle).not.toHaveBeenCalled();
+  });
+
   it("materializes the bundled CEO instruction set for default CEO agents", async () => {
     const res = await requestApp(await createApp(), (baseUrl) => request(baseUrl)
       .post("/api/companies/company-1/agents")
@@ -652,8 +675,11 @@ describe.sequential("agent skill routes", () => {
         name: "QA Agent",
         role: "engineer",
         adapterType: "claude_local",
-        adapterConfig: {
-          promptTemplate: "You are QA.",
+        adapterConfig: {},
+        instructionsBundle: {
+          files: {
+            "AGENTS.md": "You are QA.",
+          },
         },
       });
 
@@ -675,4 +701,24 @@ describe.sequential("agent skill routes", () => {
       | undefined;
     expect(approvalInput?.payload?.adapterConfig?.promptTemplate).toBeUndefined();
   });
+
+  it("rejects legacy prompt templates for hire approval payloads", async () => {
+    const res = await request(await createApp(createDb(true)))
+      .post("/api/companies/company-1/agent-hires")
+      .send({
+        name: "QA Agent",
+        role: "engineer",
+        adapterType: "claude_local",
+        adapterConfig: {
+          instructionsFilePath: "/tmp/existing/AGENTS.md",
+          promptTemplate: "You are QA.",
+          bootstrapPromptTemplate: "Bootstrap QA.",
+        },
+      });
+
+    expect(res.status, JSON.stringify(res.body)).toBe(422);
+    expect(res.body.error).toContain("New agents must use instructionsBundle/AGENTS.md");
+    expect(mockAgentService.create).not.toHaveBeenCalled();
+    expect(mockAgentInstructionsService.materializeManagedBundle).not.toHaveBeenCalled();
+  });
 });