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Author	SHA1	Message	Date
DottaandPaperclip	023f4a5d0c	fix: preserve repository cache negotiation refs (#16687) ... ## Thinking Path > - Paperclip manages agent work and its execution environments. > - A fresh repository task needs an independent checkout before its runner can start. > - The object cache from #16487 should reduce repeated network transfer. > - The cache kept Git objects but dropped remote-tracking refs during its bare clone. > - Git needs those tips to negotiate which objects it already has. > - This pull request preserves the tips in a versioned mirror cache and records explicit cache outcomes. > - The benefit is less repeated transfer and clearer evidence when a cache does not help. ## Linked Issues or Issue Description Refs #16487 and #16454. No duplicate cache-negotiation fix was found in the public PR search. **What happened?** A valid object cache could make a fresh clone slower. A controlled staging probe took 45.87 seconds and received 184.39 MB even though the reference already held the objects. An earlier probe took 52.33 seconds. An uncached clone took 20.94 seconds. `git clone --bare` copied the pristine checkout's objects, local branches, and tags, but omitted its remote-tracking refs. The source had about 1,200 remote branches. Git could not use the missing tips to negotiate those objects. **Expected behavior** Keep the pristine reference's negotiation tips. Each task must still authenticate online, use the current remote refs, and end with independent Git objects. **Steps to reproduce** 1. Clone a repository with many remote branches into a fresh checkout. 2. Publish a reference with `git clone --bare --no-hardlinks` from that checkout. 3. Clone the remote with `--reference-if-able` and `--dissociate`. 4. Compare with a reference that retains the remote-tracking tips. Use Git Trace2 and count received pack bytes. **Paperclip version or commit** The staging runtime was `27ab902d3db2770ada79c9f42a9c06e1d346f34b`, with Git 2.47.3. The cache implementation was unchanged from #16487. **Deployment mode** Docker on a persistent application volume. The probe used the application file owner and the public Paperclip repository. It did not start agent tasks or alter the application cache. ## What Changed - Publish pristine object caches with `--mirror` to retain remote-tracking tips. - Put cache format version 2 in the key and receipt. The first checkout builds a new generation. Existing generations stay under the current storage limits. - Keep the existing online authentication, current remote refs, credential and company isolation, independent objects, quotas, and fallback behavior. - Add closed Honeycomb cache outcomes and a boolean that states whether a reference was supplied to clone. - Document that a lookup hit or supplied reference does not prove Git avoided transfer. ## Verification - Controlled staging component experiment: a disposable reference copy held exactly the same 210,057 objects as the original. It added 1,187 advertised branch tips whose commits were already in those objects. - Before: 45.87 seconds and 184.39 MB received, one sample in this comparison. - After: 12.20 and 14.58 seconds; median 13.39 seconds. Received pack sizes were 1.99 and 1.95 MB. - All comparison clones used the same current remote HEAD and ended without an alternates file. - The remaining repack took 9.72–9.81 seconds. Checkout file writing took 0.86–0.96 seconds. - The staging experiment restored tips on a disposable cache copy. It did not deploy this patch or measure complete agent latency. - Confirmed both staging scratch locations were empty afterward. The original cache timestamps stayed unchanged. The temporary operator SSH key was revoked and its local files removed. - TypeScript 5.9.3 transpilation reported zero syntax diagnostics across the four changed TypeScript files. `git diff --check` passed. - The new negotiation regression fails with the old `--bare` publisher and passes with the mirror publisher. - Focused Vitest suites: 26 tests passed across repository-object-cache and execution-preparation-timing. These cover independent objects, current refs, unavailable/revoked remotes, scope separation, invalid storage, tracing isolation, and endpoint-off behavior. - The first full focused run passed 24 tests but failed its existing localhost HTTP fixture because the sandbox denied `listen` on `127.0.0.1`. The rerun with local loopback permission passed all 26 tests. - Server semantic typechecking passed with `tsc -p server/tsconfig.json --noEmit` after building the required workspace declarations. Initial attempts lacked generated dependency outputs; the completed dependency build and rerun passed. - A full application build was not run locally. CI passed: 55 checks passed and two optional checks were skipped. Greptile is 5/5 on the current head, with both findings resolved. ## Risks - Version 2 causes one cold cache rebuild. Old cache generations retain their disk usage, and the existing quota can prevent publication. - A cache still needs a full repack to produce an independent task checkout. This PR does not remove that cost. - The component experiment establishes the negotiation effect on staging. It does not establish an end-to-end agent speedup or the under-30-second goal. - The new trace fields remain behind the existing OTLP gate. Their values are closed enums or a boolean. They export no refs, paths, URLs, cache keys, credentials, or error text. ## Model Used OpenAI Codex, GPT-6 family, with code and tool use. The exact serving model ID and context window are not exposed in this session. ## 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 - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-10-18 21:28:20 -05:00
DottaandPaperclip	ce0eff7d1f	perf: reduce fresh workspace clone and sandbox staging waits (#16487) ... ## Thinking Path > - Paperclip manages AI agents and their work. > - Each run needs a private workspace and safe persistence. > - Fresh isolated repository sources download upstream Git history again. > - Sandbox staging also verifies an optional seed cache before it uploads the workspace. > - That verification holds a company lock during a full extraction and hash scan. > - This pull request reuses pristine Git objects through an authenticated remote clone. > - It also overlaps seed verification with upload and moves verification outside the publication lock. > - The benefit is less repeated transfer and less serial preparation work, with the same task isolation and recovery contract. ## Linked Issues or Issue Description **What existing behavior does this improve?** Fresh task-private repository preparation and inbound sandbox workspace staging. **Current behavior** Each isolated remote source clones the full upstream history. Optional seed verification then extracts and hashes another full tree before upload. One workspace's verification can hold the company cache lock while other workspaces wait. **Proposed behavior** Use a company and credential scoped cache of pristine upstream objects for GitHub HTTPS sources. Each task still clones from the current remote. It disconnects from the cache before publication. Run seed verification alongside upload. Hold the company lock only for final capacity checks and publication. **Reason and benefit** These operations lie on the workspace preparation path. Removing repeated Git pack transfer and serial verification can reduce startup time. Local measurements below cover these boundaries. They do not establish hosted agent latency. Related: #16425, #16454, #16398, #16461, #16468, #16473. The cache inspection and durable folder proposal in #13376 covers separate product work. ## What Changed - Add a pristine upstream Git object cache for fresh isolated GitHub HTTPS sources. Key it by company, repository and current credential fingerprint. Do not store credentials. - Keep online clone authorization and current remote refs. Use `--reference-if-able --dissociate` so task objects remain independent. A reference failure retries once online without the cache and resolves credentials again. - Cap cache storage at 64 entries and 4 GiB per company, with 2 GiB per entry. Skip contended publication. Bound priming by a cooperative five-second budget and a 4,096-entry scan allowance. Keep the existing free-space reserve. - Overlap optional seed verification and required workspace upload. Settle both before returning or deleting temporary files. Recheck quotas and company directory identity under the publication lock. - Keep the independent fresh upstream reproducibility proof, task commits, dirty source copies, ignored files, nested repositories and durable recovery behavior. - Suppress optional Git server-info generation during dissociation so generated storage passes the existing safe-expiration checks. This uses [the supported Git setting](https://git-scm.com/docs/git-config/2.43.0#Documentation/git-config.txt-repackupdateServerInfo). - Add bounded timing phases, regression coverage and two repeatable local benchmarks. No first-party Telemetry or dependency changes. ## Verification - `pnpm -r typecheck`: passed. - `pnpm build`: passed. - Affected adapter suites: 240 tests passed. Native workspace persistence/history and tracing: 33 tests passed. Server checkout/isolation/tracing batch: 53 tests passed. Final object-cache authority, path and capacity suite: 12 tests passed. These batches overlap. - Cache and expiration/restoration lifecycle batch: 34 tests passed. A direct generated-storage check covers cached clones. - Real HTTP Git fixture: a matching cache does not bypass revoked remote access. Other fixtures cover current refs/tags, hidden cached commits, independent objects after cache removal, corruption fallback, credential/company scope, quota limits and publication contention. - Initial restricted runs hit SQLite write and Unix socket permission failures. The adapter batch passed with disposable writable instance state and socket access. The first typecheck rejected the test use of `Promise.withResolvers`; typed deferred gates now use the supported library contract. - Repository benchmark on final head `9047368bf3b7fa2061e00d698b8b51cf4ae1da32`: five alternating samples, real local `file://` Git transport, synthetic 32 MiB history, no injected latency. Median 1143.8 ms to 240.5 ms; ranges 1085.7–1486.6 ms and 188.0–254.8 ms. Received Git pack bytes fell from 33,569,788 to zero. Initial cache priming took 1208.4 ms and is reported separately. - Sandbox benchmark, five alternating samples per mode on 10,000 files with real packing, extraction and verification: with a controlled 3-second transfer delay, median 9.450 s to 7.620 s (ranges 9.280–12.115 s and 7.296–7.983 s). With no injected delay, median 6.808 s to 6.450 s (ranges 6.255–7.029 s and 5.709–6.902 s). The no-delay ranges overlap; local copying competes with verification for disk. Both modes verify final tree contents, ignored-file exclusion and Git HEAD. These are synthetic local fixtures, not hosted agent runs. - Reproduce with `pnpm --filter @paperclipai/server exec tsx ../scripts/benchmark-repository-object-cache.ts` and `pnpm --filter @paperclipai/server exec tsx ../scripts/benchmark-workspace-staging.ts --baseline-ref=307eb16c0c --transfer-delay-ms=3000`. - Prior head `af766bc820` received Greptile 5/5 with no findings. Its E2E shard 7 failed in `plan-task-fixture` cleanup: company deletion raced an `activity_log` foreign key. That fixture has no provider run or Git workspace. The failure is retained here; final-head CI must pass. The corrected corruption fixture now forces a pack and verifies a real damaged archive. Current head `9047368bf3b7fa2061e00d698b8b51cf4ae1da32` has Greptile 5/5 with no review threads or findings. Final head has 55 passing checks and two optional Storybook skips. [The first workspace-shard attempt](https://github.com/paperclipai/paperclip/actions/runs/38802441857/job/116655485350) passed all 1,778 cases, then reported a late `EPIPE` from unchanged `server-utils.ts` while the ACP reuse test was active. That case mocks workspace preparation and passed locally in isolation. [Its single retry on the same commit](https://github.com/paperclipai/paperclip/actions/runs/38802441857/job/116659728034) passed, as did the dependent verification gate. The earlier E2E cleanup fixture passed on this final head. Both initial failures remain recorded here. A full local suite was not duplicated; the affected boundaries were run locally and the complete suite runs in CI. ## Risks - First cache population adds local copying. Cold clones, credential rotation, capacity exhaustion and a corrupt cache retain the online clone path. No eviction is added. Cached data is bounded, but many companies can each consume their allowance. - Individual filesystem calls and cleanup can exceed the cooperative priming budget. Failed reference clones make one additional online attempt. - Parallel verification and upload compete for disk and CPU. The local no-delay benchmark shows a smaller gain than a slow-transfer case. Verification still checks contents before cache publication, and required upload failures remain failures. - Local fixtures do not prove hosted throughput or the 15–30-second end-to-end target. The fresh checkout still writes its working tree, and model startup, copyback and other preparation costs remain. ## Model Used OpenAI Codex, GPT-6 family. The exact serving model ID and context window are not exposed in this session. Used reasoning, source editing, shell tools and test execution. ## 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 and contains no internal task identifiers - [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 - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-10-16 12:21:47 -05:00