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Author	SHA1	Message	Date
DottaandClaude Opus 5.5	c45c7cb854	fix(workspaces): ignore killed-transfer scratch in sparse checkpoints (#19730) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work > - A native run in a remote sandbox copies its workspace back to the host after the turn. A sparse checkpoint copies only changed entries, and the host validates each entry against the sandbox's own manifest > - Every Daytona transfer stages a `.paperclip-upload-<uuid>` scratch file at the sandbox workspace root and removes it only in the same process > - A control-plane kill during any transfer leaves that scratch behind. The sparse checkpoint then recorded it as a workspace file, but providers never export it. Every later copyback and every saved-work recovery attempt failed with "Workspace checkpoint payload mismatch" > - The failed recovery then left an accepted Retry showing "Paperclip is finishing the saved result" with no run > - This pull request stops recording transfer scratch, makes the checkpoint export an exact copy, names the failing entry, and gives a Retry behind a spent recovery an honest reason and a working action > - The benefit is that a restart during a transfer no longer makes a task's saved work permanently unrecoverable ## Linked Issues or Issue Description Refs #19721 (RC-50: the killed copyback owner; this PR covers the separate RC-50b cause) **What happened?** Restart-chaos waves s12/t01 and s14/t05 (Claude on Daytona). After a SIGKILL of the control plane, the native result was accepted, and then workspace copyback failed with "Workspace checkpoint payload mismatch". In s14 all 6 saved-work recovery attempts failed the same way. A Retry accepted during recovery kept `retryWait.reason = finalizing_saved_result` after the recovery budget was spent. No run was created. **Steps to reproduce** 1. Start a native Claude run in a Daytona sandbox. 2. SIGKILL the control plane while any provider transfer is in flight. 3. Let the run finish its turn and copy its workspace back. **Expected behavior** Copyback succeeds. Provider scratch is not workspace content. A Retry behind a spent recovery names the failure and can start a new recovery. **Actual behavior** The s14 sandbox (6f4a0b6a) still held `/home/daytona/paperclip-workspace/.paperclip-upload-d99fe36b-5acc-437b-96ad-85d5ff9e79c4.tar`. Its mtime was 03:29:23, the second of the K4 SIGKILL. The Daytona provider stages transfer scratch at `remoteDir`, which is the lease `remoteCwd` (the workspace root). The runtime workspace wipe deliberately preserves `.paperclip-upload-*`. The checkpoint helper (`workspace-checkpoint.ts`, `checkpointMain`) recorded the stale tar. The ordinary export excludes `.paperclip-upload*`, so the host received nothing for that entry. `validateCheckpointPayload` then threw "payload mismatch" on every attempt. The file-mode hypothesis was disproved: the sandbox umask is 022 and the scratch is mode 644. ## What Changed - `packages/adapter-utils/src/exclude-patterns.ts`: new `isSandboxTransferScratchPath`, which matches a root-level `.paperclip-upload-*` entry. This agrees with the wipe's preserve rule in `buildWorkspaceTarExtractCommand`. - `packages/adapter-utils/src/workspace-checkpoint.ts`: the sandbox checkpoint helper skips that scratch. A mismatch error now names the entry and its recorded, baseline and received forms (kind, octal mode, short hash; never contents). - `packages/adapter-utils/src/sandbox-managed-runtime.ts`: the checkpoint export requests `preserveSourceEntries: true`. The checkpoint output is an exact copy that the host validates entry by entry. An ordinary export applies the host umask and drops `._*` and `.paperclip-upload*` names at any depth. That gives the same permanent mismatch for a legitimate user file such as `._summary`, `notes/.paperclip-upload-plan.md`, or a `0775` script. - `server/src/services/explicit-native-continuation.ts` and `task-interruption-presentation.ts`: when the run's saved-work recovery is exhausted, a waiting Retry reports `saved_work_recovery_failed` with Retry available, instead of `finalizing_saved_result`. The existing task Retry path starts one new recovery generation. - `doc/execution-semantics.md`: a short additive note. ## Verification - `packages/adapter-utils/src/workspace-checkpoint-capture.test.ts` uses the real checkpoint helper and an export that behaves like Daytona's ordinary export: - Before the fix: `Workspace checkpoint payload mismatch at ".paperclip-upload-d99fe36b-….tar": sandbox recorded file mode=644 …; baseline absent; received absent`. That is the wave error. - After the fix: the scratch is not recorded, and validation passes. - A second case shows that reserved-looking user names and `0775` modes need the exact export. - `packages/adapter-utils/src/workspace-checkpoint.test.ts` is an end-to-end `prepareSandboxManagedRuntime` restore through a provider model. In that model, ordinary exports drop reserved names and apply the umask, and preserve exports copy exactly. Two red checks: - Without `preserveSourceEntries`, it fails with the mismatch on `._summary`. - Without the scratch skip, the stale tar leaks into the host workspace. - Green: the agent file, the `._summary` file and the `0775` mode arrive, and no scratch arrives. - `server/src/services/workspace-recovery-preparation-gates.test.ts`, "names a spent saved-work recovery behind an accepted Retry, and the next Retry finishes it" (s14 shape): - Red: `finalizing_saved_result` after 6 failed attempts. - Green: `saved_work_recovery_failed` with `canRetry: true`. The next Retry starts a new generation, recovery completes, and the Retry continues in exactly one new run. - Suites: adapter-utils checkpoint, capture, sandbox-managed-runtime, seed-reuse and managed-seed (168 passed). Server preparation-gates (47), explicit-native-continuation and task-interruption-presentation (455), workspace-recovery admission and retry-copyback, and native-workspace-finalizer. `tsc --noEmit` is clean for adapter-utils and server. - Live evidence: I started the stopped s14 sandbox read-only, listed its workspace, and stopped it again. No Daytona replay was run. The runner content ID of this checkout matches no built image. ## Risks - A user file named `.paperclip-upload-*` directly at the workspace root is no longer captured by a sparse checkpoint. Providers already drop that name from every ordinary export, and the runtime already reserves it at the root. - The checkpoint export now uses the provider's exact-copy mode. A workspace file with setuid, setgid or sticky bits is refused by that mode, as it is for the existing exact-copy transfers. The ordinary export would have stripped those bits and failed validation anyway. - The stale scratch tar stays in the sandbox. It is ignored, not deleted, because a concurrent transfer can own a file with the same prefix. ## Model Used - Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, through Claude Code with tool use (shell, file edits, test runs, embedded Postgres, a read-only Daytona sandbox listing). ## 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 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>	2026-11-06 22:46:16 -06:00
Devin FoleyandPaperclip	2c98c8e1e5	Fix sandbox git publishing and large workspace uploads (#8422) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work > - Sandbox and SSH runtimes need to preserve agent work across isolated execution environments > - Git-backed workspaces were being copied mostly as filesystem archives, which breaks when `.git` points outside the mounted workspace and makes sandbox agents unable to publish their own branches > - Large ignored dependency trees could also be swept into the sandbox overlay, causing multi-GB transfers and max-string failures in some sandbox clients > - This pull request makes sandbox runtime setup use a git-backed HEAD sync plus a small dirty/untracked overlay, and bounds sandbox file transfers so large archives do not need one huge string > - The benefit is that sandbox agents can commit and push from a usable git checkout without uploading dependency trees such as `node_modules` ## Linked Issues or Issue Description Refs #8395 No public duplicate issue or PR was found after searches for `sandbox git workspace`, `git push sandbox`, and `node_modules sandbox upload`. Bug report: - What happened: sandbox-backed agent workspaces could receive a `.git` file that pointed at host-only git state, leaving the sandbox unable to run normal git workflows. The sandbox overlay upload could also include ignored dependency directories, creating very large transfers. - Expected behavior: sandbox and remote runtimes should prepare a usable git-backed workspace, copy only the necessary workspace overlay, and restore git history plus file changes without depending on a host-only `.git` path. - Steps to reproduce: 1. Run an agent in a sandbox-backed workspace whose local git checkout is a worktree. 2. Ask the agent to complete a GitHub workflow that requires commit/push access. 3. Observe that git operations can fail inside the sandbox, and ignored dependency trees can be uploaded as part of the workspace overlay. - Paperclip version or commit: reproduced against `master` before this PR, base `7aa212296eb1`. - Deployment mode: local dev / sandbox-backed runtime. - Installation method: built from source. - Agent adapters involved: local adapters using shared adapter-utils runtime preparation. - Database mode: not database-related. - Access context: agent runtime. - Local verification environment: Node.js v25.6.1, pnpm 9.15.4, macOS arm64. - Privacy checklist: all pasted output was reviewed for secrets, private hostnames, local usernames, and internal instance links. ## What Changed - Added a GitHub workflow push preflight so agent runs can detect missing push credentials when a workflow explicitly needs GitHub publishing. - Added shared git workspace sync helpers for shallow HEAD import/export and dirty/untracked overlay tracking. - Updated sandbox managed runtime setup to use git history plus a selected overlay instead of uploading the full local workspace for git-backed workspaces. - Bounded sandbox archive upload/download paths so large payloads stream or chunk instead of materializing one oversized string. - Excluded `.git` and ignored dependency trees from sandbox upload, download, and restore baselines while preserving local ignored directories during sync-back. - Added focused tests for git workspace sync, sandbox overlay selection, transfer chunking, and heartbeat push-preflight behavior. ## Verification - `pnpm exec vitest run packages/adapter-utils/src/git-workspace-sync.test.ts packages/adapter-utils/src/sandbox-managed-runtime.test.ts packages/adapter-utils/src/command-managed-runtime.test.ts server/src/__tests__/heartbeat-project-env.test.ts server/src/__tests__/heartbeat-workspace-session.test.ts` - `pnpm --filter @paperclipai/adapter-utils typecheck` - `pnpm --filter @paperclipai/server typecheck` - `pnpm build` - Public-hygiene scan of the PR diff and commit messages for internal issue ids, local paths, private hostnames, and obvious token patterns. ## Risks - Medium risk: this changes sandbox runtime synchronization semantics for git-backed workspaces, especially around dirty tracked files, untracked files, deleted paths, and ignored files. - The main mitigation is focused test coverage for upload contents, restore exclusions, and git round-trip behavior. - The SSH runtime keeps the current bundle-based implementation from `master`; this PR only aligns shared excludes and sandbox behavior with that model. ## Model Used OpenAI Codex, GPT-5-based coding agent, tool-enabled shell/git/GitHub workflow, with code execution and repository inspection. ## 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] 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] All Paperclip CI gates are green - [ ] 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>	2026-06-20 22:03:55 -07:00