Harden control-plane safety and issue identifiers (#5292)

## Thinking Path

> - Paperclip relies on issue identifiers, execution policies, and agent
heartbeat rules to keep autonomous work auditable.
> - Safety checks need to reject ambiguous agent handoffs, and
identifier parsing needs to support Cloud tenant prefixes.
> - Agent instructions also need to make final-disposition rules
explicit so work does not stall in vague states.
> - This pull request isolates backend correctness and governance
hardening from the UI and recovery-system-notice branches.
> - The benefit is safer in-review transitions, better identifier
compatibility, and clearer agent operating contracts.

## What Changed

- Fixed run-aware confirmation ordering and interrupted-run state
cleanup.
- Added Cloud tenant identity bootstrap and alphanumeric issue
identifier support across shared parsing and server routes.
- Guarded agent-authored `in_review` updates unless a real review path
exists.
- Tightened heartbeat disposition instructions in adapter
utilities/default AGENTS/Paperclip skill.

## Verification

- `pnpm install --frozen-lockfile`
- `pnpm exec vitest run packages/shared/src/issue-references.test.ts
server/src/__tests__/issue-identifier-routes.test.ts
server/src/__tests__/issue-execution-policy-routes.test.ts
packages/adapter-utils/src/server-utils.test.ts` initially had the first
execution-policy test hit Vitest's 5s timeout under the parallel bundle
while the rest passed.
- `pnpm exec vitest run
server/src/__tests__/issue-execution-policy-routes.test.ts
--testTimeout=20000` passed with 10/10 tests.

- Follow-up: `pnpm run typecheck:build-gaps` passed.
- Follow-up: `pnpm --filter @paperclipai/ui typecheck` passed.
- Follow-up: `pnpm vitest run
server/src/__tests__/issue-comment-reopen-routes.test.ts
server/src/__tests__/company-portability.test.ts
server/src/__tests__/costs-service.test.ts` passed.
- Follow-up: `pnpm vitest run ui/src/context/LiveUpdatesProvider.test.ts
ui/src/lib/issue-chat-messages.test.ts
ui/src/lib/issue-reference.test.ts
ui/src/lib/issue-timeline-events.test.ts` passed.

## Risks

- Medium control-plane risk: in-review update validation changes agent
behavior. The error message is explicit and tests cover allowed review
paths.

## Model Used

- OpenAI GPT-5 Codex via Paperclip `codex_local` adapter, with
shell/git/GitHub CLI tool use.

## 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/onboarding-assets/default/AGENTS.md

@@ -4,7 +4,9 @@ You are an agent at Paperclip company.
 
 - Start actionable work in the same heartbeat. Do not stop at a plan unless the issue explicitly asks for planning.
 - Keep the work moving until it is done. If you need QA to review it, ask them. If you need your boss to review it, ask them.
-- Leave durable progress in task comments, documents, or work products, and make the next action clear before you exit.
+- Leave durable progress in task comments, documents, or work products, then update the issue to a clear final disposition before you exit.
+- Comments, documents, screenshots, work products, and `Remaining` bullets are evidence, not valid liveness paths by themselves.
+- Final disposition checklist: mark `done` when complete and verified; use `in_review` only with a real reviewer, approval, interaction, or monitor path; use `blocked` only with first-class blockers or a named unblock owner/action; create delegated follow-up issues with blockers when another agent owns the next step; keep `in_progress` only when a live continuation path exists.
 - Use child issues for parallel or long delegated work instead of polling agents, sessions, or processes.
 - Create child issues directly when you know what needs to be done. If the board/user needs to choose suggested tasks, answer structured questions, or confirm a proposal first, create an issue-thread interaction on the current issue with `POST /api/issues/{issueId}/interactions` using `kind: "suggest_tasks"`, `kind: "ask_user_questions"`, or `kind: "request_confirmation"`.
 - Use `request_confirmation` instead of asking for yes/no decisions in markdown. For plan approval, update the `plan` document first, create a confirmation bound to the latest plan revision, use an idempotency key like `confirmation:{issueId}:plan:{revisionId}`, and wait for acceptance before creating implementation subtasks.