perf(ci): rebalance server test shards and repair the weekly weight refresh (#21016)

## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - A Core image is published only after the release verification of the
same commit passes (`cloud-readiness.yml` calls `release-verify.yml`)
> - The image is ready about 3 minutes before that gate opens, so the
slowest verification job sets the staging release time
> - The slowest job is a general-server test shard: 11.8-12.7 min, while
other server shards take 8-9 min
> - The shards are balanced by a duration manifest, but the manifest has
not changed since 2026-10-31. The weekly refresh that updates it failed
on 2026-11-02 and 2026-11-09
> - About 40 newer suites per shard use the 1 s median fallback weight,
but several of them run for 90-200 s, so they pile up on one shard
> - This pull request repairs the weekly refresh and refreshes the
server weights from three current master verifications
> - The benefit is a shorter slowest server shard (predicted 10.3 -> 8.8
min of test time) on every master verification and every PR run

## Linked Issues or Issue Description

**What happened?**
The Core image publication waits about 13.5 min for source verification.
The critical path is one general-server shard. In three master
verifications (runs 43133035381, 43134251278, 43145252393) the slowest
server shard took 12.1, 11.0 and 12.7 min. The fastest took 8.0, 8.9 and
8.4 min.

**Root cause**
`scripts/general-server-shard-durations.json` came from one run on
2026-10-31. The weekly `ci-test-durations.yml` refresh failed twice:
- 2026-11-02 (run 41408033686): `gh api .../jobs/<id>/logs` failed. A
server shard log is 30-65 MB. One download took 59 s locally. Three
parallel downloads overran the 120 s `execFile` timeout.
- 2026-11-09 (run 42580964686): the refresh's own check failed.
Merged-PR sources for the Runner lane have a leading `pull` key, and the
test accepted only `run, attempt, sha, url`.

**Expected behavior**
The weekly refresh finishes and keeps the shards balanced as suites are
added.

## What Changed

- `scripts/ci/gh-api.mjs`: job-log downloads get a 15 min timeout and a
512 MB buffer. JSON calls keep 120 s. A failed call now gives a short
error and does not print the partial 60 MB log.
- `scripts/ci/pr-run-durations.mjs`: new shared `assertManifestSource`.
It accepts the optional leading `pull` key that `collectMergedPrSamples`
writes. The checked-in Runner manifest test and the collector test both
use it, so the collector format stays covered.
- `.github/workflows/ci-test-durations.yml`: refresh job timeout 20 ->
45 min (the server lanes alone fetch about 30 large logs).
- `scripts/general-server-shard-durations.json` and
`scripts/serialized-shard-durations.json`: refreshed with `node
scripts/ci/refresh-test-durations.mjs --lanes=server 43133035381
43134251278 43145252393` (median of three successful protected-master
Cloud readiness runs; 1757/1815 general files and 173/173 serialized
files measured).
- No test is added, removed, skipped or reassigned to a different lane.
No shard count changes. `docker.yml`, the Dockerfile and the PID-1 check
are not touched.

## Verification

Measured job timings (minutes from the first job start; three master
verifications):

| Job | 43133035381 | 43134251278 | 43145252393 |
| --- | --- | --- | --- |
| Slowest server shard (duration) | 7/10: 12.1 | 6/10: 11.0 | 8/10: 12.7
|
| Fastest server shard | 2/10: 8.0 | 2/10: 8.9 | 5/10: 8.4 |
| Runner chaos evals (restart/replay) | 10.2 | 11.9 | 11.0 |
| Verify Paperclip Runner (protocol) | 8.9 | 8.9 | 9.6 |
| Chat (slowest of 3) | 8.8 | 10.5 | 9.4 |
| Serialized (slowest of 5) | 9.3 | 9.5 | 9.2 |
| Build / Typecheck | 4.5 / 2.4 | 4.5 / 3.1 | 4.8 / 2.5 |
| Gate "Cloud source verified" ends | +13.5 | +13.2 | +13.9 |

- Queue to runner start is 0.5-1.1 min for every job. In a server shard,
setup (checkout, pnpm, Node, install) is about 50 s and the preflight
plus plugin-sdk build is about 8 s. The test step is the rest (9-11.8
min). Setup is not worth caching.
- Shard prediction, using the refreshed medians as the cost of each file
and the 3 fork workers per shard:
- general-server, 10 shards: old weights max 10.3 / min 8.1 min; new
weights 8.8 / 8.8 min.
- serialized, 5 shards: old weights max 8.2 / min 4.6 min; new weights
6.6 / 6.6 min.
- The old-weight prediction matches what CI saw: predicted 10.3 and 9.9
min for shards 7/10 and 6/10, measured test steps 11.25 and 10.1 min in
run 43133035381.
- Red/green:
- `node --test --test-name-pattern="gh api"
scripts/ci/test-selection-pr-timings.test.mjs` failed before the fix
(`log timeout 120000`) and passes after it.
- With a `pull` key in the Runner manifest sources, the old "package
lane manifest" test failed with the same assertion as run 42580964686.
The new test passes.
- The refresh script, which died before the fix, completed locally in 8
min after it.
- `node --test scripts/ci/test-selection-timings.test.mjs
scripts/ci/test-selection-pr-timings.test.mjs
scripts/__tests__/run-vitest-stable-shard.test.mjs
scripts/__tests__/e2e-shard.test.mjs`: 76/76 pass. This includes the
complete, non-overlapping shard cover checks.
- `actionlint .github/workflows/ci-test-durations.yml`: clean.
- Not run: the release-verify workflow itself, the scheduled refresh
workflow, and the Runner/e2e lane refresh. The shard times above are
predictions from logged per-file timings, not a measured CI run on this
branch.

## Risks

- Low risk. Weights only move files between shards of the same lane. The
shard tests prove every file still runs exactly once.
- The predicted gain is about 1.5 min on the slowest server shard
(12-12.7 -> about 10.5 min job time). The gate then waits for
"Pre-release Runner chaos evals / Restart, replay, trace, and recovery
faults" (10.2-11.9 min). So the expected gate saving is about 1 min
(13.5 -> about 12.5 min), not the full 1.5 min. Run-to-run noise on a
shard is about ±1 min.
- A larger log timeout can make a stuck download wait up to 15 min. The
45 min job timeout still bounds the run.

Candidates for the owner (not changed here):
- The chaos-eval job is now the bound. Its "server finalization" step
takes 7-9 min. Decide if it must gate image publication, or split it.
- Server shard logs are up to 811k lines, mostly repeated stack traces
from `server/src/services/execution-preparation-timing.ts`. That slows
log upload and this refresh.
- 9 test files run over 180 s (largest:
`chat-channels.integration.test.ts` 429 s,
`heartbeat-process-recovery.test.ts` 344 s). One file cannot be split
across shards.

> 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

- Claude Opus 5.5 (`claude-opus-5-5`), via Claude Code with tool use
(shell, GitHub CLI read-only). Standard reasoning mode.

## 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 searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` / `Refs #` OR (b) described the issue in-PR following the relevant
issue template
- [x] I have not referenced internal/instance-local Paperclip issues or
links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip`
URLs)
- [x] My branch name describes the change (e.g. `docs/...`, `fix/...`)
and contains no internal Paperclip ticket id or instance-derived details
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [ ] All Paperclip CI gates are green
- [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [ ] I will address all Greptile and reviewer comments before
requesting merge

Related: #19650 (earlier repair of the weekly refresh), #21013 (Core
image publish time; separate files).

🤖 Generated with [Claude Code](https://claude.com/claude-code)

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>

.github/workflows/ci-test-durations.yml

@@ -18,7 +18,9 @@ jobs:
   refresh:
     if: github.repository == 'paperclipai/paperclip' && github.repository_id == '1170821064' && github.ref == 'refs/heads/master'
     runs-on: ubuntu-latest
-    timeout-minutes: 20
+    # Server shard logs are 30-65 MB each and the master lanes alone fetch
+    # about 30 of them, three at a time; 20 minutes left no headroom.
+    timeout-minutes: 45
     steps:
       - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1
         with: