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Author	SHA1	Message	Date
Devin FoleyandPaperclip	721541c41d	Fix sandbox restore index drift (#8595) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - Sandboxed agents can do useful work in a remote workspace, then export that result back to a host review checkout. > - A restore can leave the host checkout's index stale even when the sandbox content and committed state are correct. > - That drift makes reviewers see misleading missing-file or dirty-state results after sandbox execution. > - This pull request repairs the host index refresh path and surfaces a clean/dirty restore signal during finalization. > - The benefit is more reliable review checkouts and clearer sandbox finalization status. ## Linked Issues or Issue Description Refs #248 No exact public GitHub issue was found for this restore/index consistency fix. The underlying bug is that a sandbox restore can update host working-tree content without leaving the host git index aligned, so local review tooling may report stale deletions or misleading dirtiness. This PR keeps the restore/export path consistent and reports the resulting clean/dirty state. GitHub search performed for related or duplicate work: `sandbox runtime status`, `sandbox restore index`, and `runtime progress`. No direct duplicate PR was found. ## What Changed - Refreshed git workspace sync/index handling after sandbox restore/export operations. - Added finalization status that reports whether the restored host checkout is clean or dirty. - Preserved sandbox-managed runtime progress callbacks around restore and finalization. - Added adapter-utils tests covering the host index drift repair and clean/dirty finalization signal. ## Verification - Local PII scan before push: high-confidence secret patterns, internal issue links, local user paths, and private URL patterns checked across all three split diffs; no real secrets or internal links found. - `git diff --check feat/sandbox-runtime-status..fix/sandbox-restore-index-sync` - `pnpm exec vitest run packages/adapter-utils/src/sandbox-managed-runtime.test.ts` — 1 file, 10 tests passed. - `pnpm run typecheck` passed on `fix/sandbox-restore-index-sync`. - `pnpm run build` passed on `fix/sandbox-restore-index-sync`; Vite reported existing CSS `::highlight` and chunk-size warnings. - `pnpm run test:run` was attempted on `fix/sandbox-restore-index-sync`; it failed in two unrelated broad-suite tests. One depends on this host's Git default branch behavior, and one depends on local Claude model-discovery environment. The changed focused suite above passes. ## Risks - Git index refresh behavior needs to remain conservative so it does not hide real uncommitted user changes. - The clean/dirty finalization signal is diagnostic; it should not by itself mark a sandbox run successful or failed. - This PR is stacked on the runtime-status branch so finalization progress can reuse the same callback path. > 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 GPT-5 via Codex coding agent, with shell/tool execution in a local worktree. Exact context-window metadata is not exposed 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 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>	2026-06-24 23:21:13 -07:00
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