Stabilize serialized server route tests (#4448)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies
> - The server route suite is a core confidence layer for auth, issue
context, and workspace runtime behavior
> - Some route tests were doing extra module/server isolation work that
made local runs slower and more fragile
> - The stable Vitest runner also needs to pass server-relative exclude
paths to avoid accidentally re-including serialized suites
> - This pull request tightens route test isolation and runner
serialization behavior
> - The benefit is more reliable targeted and stable-route test
execution without product behavior changes

## What Changed

- Updated `run-vitest-stable.mjs` to exclude serialized server tests
using server-relative paths.
- Forced the server Vitest config to use a single worker in addition to
isolated forks.
- Simplified agent permission route tests to create per-request test
servers without shared server lifecycle state.
- Stabilized issue goal context route mocks by using static mocked
services and a sequential suite.
- Re-registered workspace runtime route mocks before cache-busted route
imports.

## Verification

- `pnpm exec vitest run --project @paperclipai/server
server/src/__tests__/agent-permissions-routes.test.ts
server/src/__tests__/issues-goal-context-routes.test.ts
server/src/__tests__/workspace-runtime-routes-authz.test.ts --pool=forks
--poolOptions.forks.isolate=true`
- `node --check scripts/run-vitest-stable.mjs`

## Risks

- Low risk. This is test infrastructure only.
- The stable runner path fix changes which tests are excluded from the
non-serialized server batch, matching the server project root that
Vitest applies internally.

> 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 coding agent, tool-enabled with
shell/GitHub/Paperclip API access. Context window was not reported by
the runtime.

## 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>

scripts/run-vitest-stable.mjs

@@ -5,6 +5,7 @@ import os from "node:os";
 import path from "node:path";
 
 const repoRoot = process.cwd();
+const serverRoot = path.join(repoRoot, "server");
 const serverTestsDir = path.join(repoRoot, "server", "src", "__tests__");
 const nonServerProjects = [
   "@paperclipai/shared",
@@ -63,6 +64,10 @@ function toRepoPath(file) {
   return path.relative(repoRoot, file).split(path.sep).join("/");
 }
 
+function toServerPath(file) {
+  return path.relative(serverRoot, file).split(path.sep).join("/");
+}
+
 function isRouteOrAuthzTest(file) {
   if (routeTestPattern.test(file)) {
     return true;
@@ -99,10 +104,13 @@ function runVitest(args, label) {
 
 const routeTests = walk(serverTestsDir)
   .filter((file) => isRouteOrAuthzTest(toRepoPath(file)))
-  .map((file) => ({ repoPath: toRepoPath(file) }))
+  .map((file) => ({
+    repoPath: toRepoPath(file),
+    serverPath: toServerPath(file),
+  }))
   .sort((a, b) => a.repoPath.localeCompare(b.repoPath));
 
-const excludeRouteArgs = routeTests.flatMap((file) => ["--exclude", file.repoPath]);
+const excludeRouteArgs = routeTests.flatMap((file) => ["--exclude", file.serverPath]);
 for (const project of nonServerProjects) {
   runVitest(["--project", project], `non-server project ${project}`);
 }