[codex] Add issue subtree pause, cancel, and restore controls (#4332)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies.
> - This branch extends the issue control-plane so board operators can
pause, cancel, and later restore whole issue subtrees while keeping
descendant execution and wake behavior coherent.
> - That required new hold state in the database, shared contracts,
server routes/services, and issue detail UI controls so subtree actions
are durable and auditable instead of ad hoc.
> - While this branch was in flight, `master` advanced with new
environment lifecycle work, including a new `0065_environments`
migration.
> - Before opening the PR, this branch had to be rebased onto
`paperclipai/paperclip:master` without losing the existing
subtree-control work or leaving conflicting migration numbering behind.
> - This pull request rebases the subtree pause/cancel/restore feature
cleanly onto current `master`, renumbers the hold migration to
`0066_issue_tree_holds`, and preserves the full branch diff in a single
PR.
> - The benefit is that reviewers get one clean, mergeable PR for the
subtree-control feature instead of stale branch history with migration
conflicts.

## What Changed

- Added durable issue subtree hold data structures, shared
API/types/validators, server routes/services, and UI flows for subtree
pause, cancel, and restore operations.
- Added server and UI coverage for subtree previewing, hold
creation/release, dependency-aware scheduling under holds, and issue
detail subtree controls.
- Rebased the branch onto current `paperclipai/paperclip:master` and
renumbered the branch migration from `0065_issue_tree_holds` to
`0066_issue_tree_holds` so it no longer conflicts with upstream
`0065_environments`.
- Added a small follow-up commit that makes restore requests return `200
OK` explicitly while keeping pause/cancel hold creation at `201
Created`, and updated the route test to match that contract.

## Verification

- `pnpm --filter @paperclipai/db typecheck`
- `pnpm --filter @paperclipai/shared typecheck`
- `pnpm --filter @paperclipai/server typecheck`
- `pnpm --filter @paperclipai/ui typecheck`
- `cd server && pnpm exec vitest run
src/__tests__/issue-tree-control-routes.test.ts
src/__tests__/issue-tree-control-service.test.ts
src/__tests__/issue-tree-control-service-unit.test.ts
src/__tests__/heartbeat-dependency-scheduling.test.ts`
- `cd ui && pnpm exec vitest run src/components/IssueChatThread.test.tsx
src/pages/IssueDetail.test.tsx`

## Risks

- This is a broad cross-layer change touching DB/schema, shared
contracts, server orchestration, and UI; regressions are most likely
around subtree status restoration or wake suppression/resume edge cases.
- The migration was renumbered during PR prep to avoid the new upstream
`0065_environments` conflict. Reviewers should confirm the final
`0066_issue_tree_holds` ordering is the only hold-related migration that
lands.
- The issue-tree restore endpoint now responds with `200` instead of
relying on implicit behavior, which is semantically better for a restore
operation but still changes an API detail that clients or tests could
have assumed.

> 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 coding agent in the Paperclip Codex runtime (GPT-5-class
tool-using coding model; exact deployment ID/context window is not
exposed inside this session).

## 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
- [ ] 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>

ui/src/components/IssuesList.tsx

@@ -52,10 +52,11 @@ import { Button } from "@/components/ui/button";
 import { Input } from "@/components/ui/input";
 import { Popover, PopoverTrigger, PopoverContent } from "@/components/ui/popover";
 import { Collapsible, CollapsibleContent } from "@/components/ui/collapsible";
-import { CircleDot, Plus, ArrowUpDown, Layers, Check, ChevronRight, List, ListTree, Columns3, User, Search } from "lucide-react";
+import { CircleDot, Plus, ArrowUpDown, Layers, Check, ChevronRight, List, ListTree, Columns3, User, Search, CircleSlash2 } from "lucide-react";
 import { KanbanBoard } from "./KanbanBoard";
 import { buildIssueTree, countDescendants } from "../lib/issue-tree";
 import { buildSubIssueDefaultsForViewer } from "../lib/subIssueDefaults";
+import { statusBadge } from "../lib/status-colors";
 import type { Issue, Project } from "@paperclipai/shared";
 const ISSUE_SEARCH_DEBOUNCE_MS = 250;
 const ISSUE_SEARCH_RESULT_LIMIT = 200;
@@ -208,6 +209,8 @@ interface IssuesListProps {
   baseCreateIssueDefaults?: Record<string, unknown>;
   createIssueLabel?: string;
   enableRoutineVisibilityFilter?: boolean;
+  mutedIssueIds?: Set<string>;
+  issueBadgeById?: Map<string, string>;
   onSearchChange?: (search: string) => void;
   onUpdateIssue: (id: string, data: Record<string, unknown>) => void;
 }
@@ -291,6 +294,8 @@ export function IssuesList({
   baseCreateIssueDefaults,
   createIssueLabel,
   enableRoutineVisibilityFilter = false,
+  mutedIssueIds,
+  issueBadgeById,
   onSearchChange,
   onUpdateIssue,
 }: IssuesListProps) {
@@ -945,6 +950,8 @@ export function IssuesList({
                   const useDeferredRowRendering = !(hasChildren && isExpanded);
                   const issueProject = issue.projectId ? projectById.get(issue.projectId) ?? null : null;
                   const parentIssue = issue.parentId ? issueById.get(issue.parentId) ?? null : null;
+                  const issueBadge = issueBadgeById?.get(issue.id);
+                  const isMutedIssue = mutedIssueIds?.has(issue.id) === true;
                   const assigneeUserProfile = issue.assigneeUserId
                     ? companyUserProfileMap.get(issue.assigneeUserId) ?? null
                     : null;
@@ -979,11 +986,32 @@ export function IssuesList({
                       <IssueRow
                         issue={issue}
                         issueLinkState={issueLinkState}
-                        titleSuffix={hasChildren && !isExpanded ? (
-                          <span className="ml-1.5 text-xs text-muted-foreground">
-                            ({totalDescendants} sub-task{totalDescendants !== 1 ? "s" : ""})
-                          </span>
-                        ) : undefined}
+                        titleSuffix={(
+                          <>
+                            {hasChildren && !isExpanded ? (
+                              <span className="ml-1.5 text-xs text-muted-foreground">
+                                ({totalDescendants} sub-task{totalDescendants !== 1 ? "s" : ""})
+                              </span>
+                            ) : null}
+                            {issueBadge ? (
+                              issueBadge === "Paused" ? (
+                                <span
+                                  className={cn("ml-1.5 inline-flex items-center gap-1 rounded-full px-1.5 py-0.5 text-[10px] font-medium", statusBadge.paused)}
+                                  aria-label="Paused"
+                                  title="Paused"
+                                >
+                                  <CircleSlash2 className="h-3 w-3" />
+                                  Paused
+                                </span>
+                              ) : (
+                                <span className="ml-1.5 inline-flex items-center rounded-full border border-amber-500/40 bg-amber-500/10 px-1.5 py-0.5 text-[10px] font-medium text-amber-700 dark:text-amber-300">
+                                  {issueBadge}
+                                </span>
+                              )
+                            ) : null}
+                          </>
+                        )}
+                        className={isMutedIssue ? "opacity-70" : undefined}
                         mobileLeading={
                           hasChildren ? (
                             <button type="button" onClick={toggleCollapse}>