[codex] Add structured issue-thread interactions (#4244)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies.
> - Operators supervise that work through issues, comments, approvals,
and the board UI.
> - Some agent proposals need structured board/user decisions, not
hidden markdown conventions or heavyweight governed approvals.
> - Issue-thread interactions already provide a natural thread-native
surface for proposed tasks and questions.
> - This pull request extends that surface with request confirmations,
richer interaction cards, and agent/plugin/MCP helpers.
> - The benefit is that plan approvals and yes/no decisions become
explicit, auditable, and resumable without losing the single-issue
workflow.

## What Changed

- Added persisted issue-thread interactions for suggested tasks,
structured questions, and request confirmations.
- Added board UI cards for interaction review, selection, question
answers, and accept/reject confirmation flows.
- Added MCP and plugin SDK helpers for creating interaction cards from
agents/plugins.
- Updated agent wake instructions, onboarding assets, Paperclip skill
docs, and public docs to prefer structured confirmations for
issue-scoped decisions.
- Rebased the branch onto `public-gh/master` and renumbered branch
migrations to `0063` and `0064`; the idempotency migration uses `ADD
COLUMN IF NOT EXISTS` for old branch users.

## Verification

- `git diff --check public-gh/master..HEAD`
- `pnpm exec vitest run packages/adapter-utils/src/server-utils.test.ts
packages/mcp-server/src/tools.test.ts
packages/shared/src/issue-thread-interactions.test.ts
ui/src/lib/issue-thread-interactions.test.ts
ui/src/lib/issue-chat-messages.test.ts
ui/src/components/IssueThreadInteractionCard.test.tsx
ui/src/components/IssueChatThread.test.tsx
server/src/__tests__/issue-thread-interaction-routes.test.ts
server/src/__tests__/issue-thread-interactions-service.test.ts
server/src/services/issue-thread-interactions.test.ts` -> 9 files / 79
tests passed
- `pnpm -r typecheck` -> passed, including `packages/db` migration
numbering check

## Risks

- Medium: this adds a new issue-thread interaction model across
db/shared/server/ui/plugin surfaces.
- Migration risk is reduced by placing this branch after current master
migrations (`0063`, `0064`) and making the idempotency column add
idempotent for users who applied the old branch numbering.
- UI interaction behavior is covered by component tests, but this PR
does not include browser screenshots.

> 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-class coding agent runtime. Exact model ID and
context window are not exposed in this Paperclip run; tool use and local
shell/code execution were enabled.

## 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
- [ ] 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>

cli/src/__tests__/company-import-export-e2e.test.ts

@@ -503,5 +503,5 @@ describeEmbeddedPostgres("paperclipai company import/export e2e", () => {
 
     expect(importedFromZip.company.action).toBe("created");
     expect(importedFromZip.agents.some((agent) => agent.action === "created")).toBe(true);
-  }, 60_000);
+  }, 90_000);
 });

cli/src/__tests__/worktree.test.ts

@@ -599,7 +599,7 @@ describe("worktree helpers", () => {
         fs.rmSync(tempRoot, { recursive: true, force: true });
       }
     },
-    20000,
+    30000,
   );
 
   it("avoids ports already claimed by sibling worktree instance configs", async () => {
@@ -881,7 +881,7 @@ describe("worktree helpers", () => {
       }
       fs.rmSync(tempRoot, { recursive: true, force: true });
     }
-  }, 20_000);
+  }, 30_000);
 
   it("restores the current worktree config and instance data if reseed fails", async () => {
     const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-reseed-rollback-"));
@@ -1038,7 +1038,7 @@ describe("worktree helpers", () => {
       execFileSync("git", ["worktree", "remove", "--force", worktreePath], { cwd: repoRoot, stdio: "ignore" });
       fs.rmSync(tempRoot, { recursive: true, force: true });
     }
-  });
+  }, 15_000);
 
   it("creates and initializes a worktree from the top-level worktree:make command", async () => {
     const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-make-"));