[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/__tests__/worktree-config.test.ts

@@ -210,6 +210,56 @@ describe("worktree config repair", () => {
     expect(repairedConfig.database.embeddedPostgresPort).toBe(54331);
   });
 
+  it("ignores stale migrated env paths when the dev runner resolved the local config", async () => {
+    const tempRoot = await fs.mkdtemp(path.join(os.tmpdir(), "paperclip-worktree-migrated-env-"));
+    const worktreeRoot = path.join(tempRoot, "PAP-9940-what-can-we-learn");
+    const paperclipDir = path.join(worktreeRoot, ".paperclip");
+    const configPath = path.join(paperclipDir, "config.json");
+    const envPath = path.join(paperclipDir, ".env");
+    const oldHome = "/old/home/.paperclip-worktrees";
+    const isolatedHome = path.join(tempRoot, ".paperclip-worktrees");
+
+    await fs.mkdir(paperclipDir, { recursive: true });
+    await fs.writeFile(configPath, JSON.stringify(buildLegacyConfig(oldHome), null, 2) + "\n", "utf8");
+    await fs.writeFile(
+      envPath,
+      [
+        "# Paperclip environment variables",
+        "PAPERCLIP_HOME=/old/home/.paperclip-worktrees",
+        "PAPERCLIP_INSTANCE_ID=pap-9940-what-can-we-learn",
+        "PAPERCLIP_CONFIG=/old/home/paperclip/.paperclip/worktrees/PAP-9940-what-can-we-learn/.paperclip/config.json",
+        "PAPERCLIP_CONTEXT=/old/home/.paperclip-worktrees/context.json",
+        "PAPERCLIP_IN_WORKTREE=true",
+        "PAPERCLIP_WORKTREE_NAME=PAP-9940-what-can-we-learn",
+        "",
+      ].join("\n"),
+      "utf8",
+    );
+
+    process.chdir(worktreeRoot);
+    process.env.PAPERCLIP_IN_WORKTREE = "true";
+    process.env.PAPERCLIP_CONFIG = configPath;
+    process.env.PAPERCLIP_WORKTREES_DIR = isolatedHome;
+    delete process.env.PAPERCLIP_HOME;
+    delete process.env.PAPERCLIP_INSTANCE_ID;
+    delete process.env.PAPERCLIP_CONTEXT;
+
+    const result = maybeRepairLegacyWorktreeConfigAndEnvFiles();
+    const repairedConfig = JSON.parse(await fs.readFile(configPath, "utf8"));
+    const repairedEnv = await fs.readFile(envPath, "utf8");
+    const instanceRoot = path.join(isolatedHome, "instances", "pap-9940-what-can-we-learn");
+
+    expect(result).toEqual({
+      repairedConfig: true,
+      repairedEnv: true,
+    });
+    expect(repairedConfig.database.embeddedPostgresDataDir).toBe(path.join(instanceRoot, "db"));
+    expect(repairedConfig.secrets.localEncrypted.keyFilePath).toBe(path.join(instanceRoot, "secrets", "master.key"));
+    expect(repairedEnv).toContain(`PAPERCLIP_HOME=${JSON.stringify(isolatedHome)}`);
+    expect(repairedEnv).toContain(`PAPERCLIP_CONFIG=${JSON.stringify(configPath)}`);
+    expect(repairedEnv).not.toContain("/old/home");
+  });
+
   it("does not persist transient runtime home overrides over repo-local worktree env", async () => {
     const tempRoot = await fs.mkdtemp(path.join(os.tmpdir(), "paperclip-worktree-runtime-override-"));
     const isolatedHome = path.join(tempRoot, ".paperclip-worktrees");
@@ -508,6 +558,8 @@ describe("worktree config repair", () => {
     process.env.PAPERCLIP_HOME = isolatedHome;
     process.env.PAPERCLIP_INSTANCE_ID = "pap-878-create-a-mine-tab-in-inbox";
     process.env.PAPERCLIP_CONFIG = configPath;
+    delete process.env.PORT;
+    delete process.env.DATABASE_URL;
 
     maybePersistWorktreeRuntimePorts({
       serverPort: 3103,
@@ -590,6 +642,8 @@ describe("worktree config repair", () => {
     process.env.PAPERCLIP_HOME = isolatedHome;
     process.env.PAPERCLIP_INSTANCE_ID = "pap-125-public-base-url";
     process.env.PAPERCLIP_CONFIG = configPath;
+    delete process.env.PORT;
+    delete process.env.DATABASE_URL;
 
     maybePersistWorktreeRuntimePorts({
       serverPort: 3103,