Fix flaky runWithRateLimit test by using fake timers

The 'throttles the task when the cache is populated recently' test was
flaky because it used real time with a 1-second timeout window. Under CI
load, the time between filling the rate limit cache and checking it could
exceed 1 second, causing the old occurrences to be swept out and the
rate limit to no longer be exceeded.

Fix by using vi.useFakeTimers() to freeze time during the test, matching
the pattern already used by the 'cache is populated but outdated' test
in the same describe block. The existing afterEach hook already calls
vi.useRealTimers() for cleanup.

Also applied the same fix to the 'rate limit isn't used up' test to
prevent the same class of flake.

Author: gonzaloriestra

packages/cli-kit/src/private/node/conf-store.test.ts

@@ -474,6 +474,7 @@ describe('runWithRateLimit', () => {
   test('throttles the task when the cache is populated recently', async () => {
     await inTemporaryDirectory(async (cwd) => {
       // Given
+      vi.useFakeTimers()
       const config = new LocalStorage<any>({cwd})
       for (let i = 0; i < limit; i++) {
         // eslint-disable-next-line no-await-in-loop
@@ -511,6 +512,7 @@ describe('runWithRateLimit', () => {
   test("runs the task as usual when the cache is populated recently but the rate limit isn't used up", async () => {
     await inTemporaryDirectory(async (cwd) => {
       // Given
+      vi.useFakeTimers()
       const config = new LocalStorage<any>({cwd})
       // Run the task once, but the rate limit is 2
       await runWithRateLimit(