[codex] Bundle local branch fixes from PAP-10032 (#6604)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies.
> - This branch accumulated multiple already-tested control-plane,
adapter runtime, invite, workspace, plugin, and UI quality fixes on the
primary Paperclip checkout.
> - `origin/master` advanced while those commits were still local, so
the branch needed to be preserved and reconciled before review.
> - Splitting the branch commit-by-commit against the new base produced
overlapping conflicts with recently merged upstream PRs.
> - This pull request keeps the remaining branch as one standalone PR
because the final diff is 38 files after removing screenshot artifacts,
under Greptile's 100-file cap, and can be merged independently after
review.
> - The benefit is that none of the local work is lost, the branch is
now based on current `origin/master`, and reviewers can evaluate the
reconciled changes in one place.

## What Changed

- Merged the local accumulated branch with current `origin/master` and
resolved the invite-flow overlaps from the newer upstream companies
query helper.
- Preserved the local fixes for invite existing-member behavior, invite
link copy fallback, reusable workspace selection, worktree auth, static
SPA fallback, markdown wrapping, plugin slot registration, cloud
upstream UX/server polish, project sorting, and related tests.
- Removed screenshot artifacts from the PR per review request.
- Kept the PR under the requested file limit: 38 files changed, with no
`pnpm-lock.yaml` or `.github/workflows/*` changes.

## Verification

- `NODE_ENV=test pnpm exec vitest run
ui/src/pages/CompanyInvites.test.tsx ui/src/pages/InviteLanding.test.tsx
ui/src/pages/Projects.test.tsx ui/src/plugins/slots.test.ts
ui/src/components/MarkdownBody.test.tsx
server/src/__tests__/invite-accept-existing-member.test.ts
server/src/__tests__/static-index-html.test.ts
server/src/__tests__/execution-workspaces-service.test.ts
server/src/__tests__/better-auth.test.ts
server/src/__tests__/worktree-config.test.ts`
- `NODE_ENV=test pnpm --filter @paperclipai/ui typecheck`
- `NODE_ENV=test pnpm --filter @paperclipai/server typecheck`
- Confirmed `git diff --name-only origin/master...HEAD | wc -l` is `38`.
- Confirmed no PR diff entries match `pnpm-lock.yaml`,
`.github/workflows/*`, or `screenshots/*`.

## Risks

- Medium review risk because this is a bundled rescue PR rather than
several narrow feature PRs.
- Invite flow and company cache behavior overlapped with newer upstream
changes; the merge resolution intentionally keeps the shared
`companiesListQueryOptions` helper while preserving local
existing-member invite behavior.
- Visual review evidence is no longer attached in-repo because
screenshots were removed from this PR per review request.

> 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-based coding agent, with repository tool access,
terminal execution, and git/GitHub CLI operations.

## 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] UI screenshots were intentionally removed from this PR per review
request
- [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>
Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>
Co-authored-by: CodexCoder <codexcoder@paperclip.local>

server/src/services/cloud-upstreams.ts

@@ -103,6 +103,7 @@ type UpstreamTransferManifest = {
   idempotencyKey: string;
   generatedAt: string;
   entityCount: number;
+  perEntityTypeCounts: Record<string, number>;
   entities: UpstreamTransferEntityRecord[];
   chunks: Array<Omit<LocalUpstreamExportChunk, "payload"> & { manifestHash: NormalizedSha256 }>;
   warnings: UpstreamTransferWarning[];
@@ -914,6 +915,7 @@ function buildLocalUpstreamExportBundle(input: {
     idempotencyKey: input.idempotencyKey,
     generatedAt: new Date(0).toISOString(),
     entityCount: entities.length,
+    perEntityTypeCounts: countEntityTypesForManifest(entities),
     entities: entities.map((entity) => entity.record),
     chunks: chunksWithoutManifestHash.map(({ payload: _payload, ...chunk }) => chunk),
     warnings: input.warnings ?? [],
@@ -931,6 +933,15 @@ function buildLocalUpstreamExportBundle(input: {
   };
 }
 
+function countEntityTypesForManifest(entities: LocalUpstreamExportEntity[]): Record<string, number> {
+  const counts: Record<string, number> = {};
+  for (const entity of entities) {
+    const entityType = entity.record.key.sourceEntityType;
+    counts[entityType] = (counts[entityType] ?? 0) + 1;
+  }
+  return counts;
+}
+
 function buildLocalChunks(entities: LocalUpstreamExportEntity[], maxEntitiesPerChunk: number): LocalUpstreamExportChunk[] {
   if (!Number.isInteger(maxEntitiesPerChunk) || maxEntitiesPerChunk < 1) {
     throw new Error("maxEntitiesPerChunk must be a positive integer");

server/src/services/execution-workspaces.ts

@@ -2,7 +2,7 @@ import { execFile } from "node:child_process";
 import fs from "node:fs/promises";
 import path from "node:path";
 import { promisify } from "node:util";
-import { and, desc, eq, inArray } from "drizzle-orm";
+import { and, desc, eq, inArray, isNull } from "drizzle-orm";
 import type { Db } from "@paperclipai/db";
 import { executionWorkspaces, issues, projects, projectWorkspaces, workspaceRuntimeServices } from "@paperclipai/db";
 import type {
@@ -344,12 +344,18 @@ function toExecutionWorkspace(
   };
 }
 
-function toExecutionWorkspaceSummary(row: Pick<ExecutionWorkspaceRow, "id" | "name" | "mode" | "projectWorkspaceId">): ExecutionWorkspaceSummary {
+function toExecutionWorkspaceSummary(
+  row: Pick<ExecutionWorkspaceRow, "id" | "name" | "mode" | "status" | "cwd" | "branchName" | "projectWorkspaceId" | "lastUsedAt">,
+): ExecutionWorkspaceSummary {
   return {
     id: row.id,
     name: row.name,
     mode: row.mode as ExecutionWorkspaceSummary["mode"],
+    status: row.status as ExecutionWorkspaceSummary["status"],
+    cwd: row.cwd ?? null,
+    branchName: row.branchName ?? null,
     projectWorkspaceId: row.projectWorkspaceId ?? null,
+    lastUsedAt: row.lastUsedAt,
   };
 }
 
@@ -412,6 +418,8 @@ export function executionWorkspaceService(db: Db) {
     }
     if (filters?.reuseEligible) {
       conditions.push(inArray(executionWorkspaces.status, ["active", "idle", "in_review"]));
+      conditions.push(isNull(executionWorkspaces.closedAt));
+      conditions.push(inArray(executionWorkspaces.mode, ["isolated_workspace", "operator_branch", "adapter_managed", "cloud_sandbox"]));
     }
     return conditions;
   }
@@ -452,7 +460,11 @@ export function executionWorkspaceService(db: Db) {
           id: executionWorkspaces.id,
           name: executionWorkspaces.name,
           mode: executionWorkspaces.mode,
+          status: executionWorkspaces.status,
+          cwd: executionWorkspaces.cwd,
+          branchName: executionWorkspaces.branchName,
           projectWorkspaceId: executionWorkspaces.projectWorkspaceId,
+          lastUsedAt: executionWorkspaces.lastUsedAt,
         })
         .from(executionWorkspaces)
         .where(and(...conditions))

server/src/services/plugin-worker-manager.ts

@@ -559,7 +559,9 @@ export function createPluginWorkerHandle(
       (message as { paperclipInvocationId?: unknown }).paperclipInvocationId,
     );
     if (!invocationId) {
-      return activeInvocations.size > 0 ? { invalidInvocationScope: true } : {};
+      const hasActiveInvocation = activeInvocations.size > 0 ||
+        Array.from(pendingRequests.values()).some((pending) => pending.invocationId);
+      return hasActiveInvocation ? { invalidInvocationScope: true } : {};
     }
     const entry = activeInvocations.get(invocationId);
     if (!entry) return { invalidInvocationScope: true };