mirror of
https://github.com/paperclipai/paperclip.git
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## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work > - A project can attach more than one repository. The task workspace keeps the selected repository at its root and puts the other project repositories under `.paperclip-repositories/<name>-<key>`, each with its own `.git` > - Agents can run on an SSH execution environment. Paperclip copies the task workspace to the remote host before the run and restores it after the run > - The SSH copy excludes `.git` at every depth, but the restore baseline excludes it only at the workspace root > - So the other project repositories reach the remote host without Git, and the restore then deletes their `.git` directories on the Paperclip host > - The next run of the same task fails during workspace setup, and the agent cannot commit to those repositories on the remote host > - This pull request transports each project repository as a Git workspace of its own, the same way the sandbox path already handles them > - The benefit is that multi-repository projects work on SSH environments across consecutive runs ## Linked Issues or Issue Description Refs #11632 (SSH workspace transfer exclude list). Related SSH workspace PRs: #14233, #14428, #14472. I found no issue or PR for this bug. **What happened?** A project has two repositories and its agent runs on an SSH environment. After the first run, the second repository under `.paperclip-repositories/` has no `.git` directory on the Paperclip host. The next run of the same task fails during setup with `Managed workspace path "…/.paperclip-repositories/<repo>" already exists but is not a git checkout.` On the remote host, `git` inside that repository resolves to the parent repository. **Expected behavior** Each project repository reaches the remote host as a Git checkout with its local changes. Remote commits and edits come back after the run. The next run of the same task starts normally. **Steps to reproduce** 1. Create a project with two repositories. 2. Configure an SSH execution environment and make it the agent's default environment. 3. Assign a task to the agent and let it run once. 4. Look at `.paperclip-repositories/<repo>` in the task workspace: `.git` is gone. 5. Wake the agent on the same task again: the run fails with `setup_failed`. **Paperclip version or commit** Reproduced on `v2026.916.1` and on `master` (`5edf55d73`). **Deployment mode** Self-hosted (Docker), authenticated, with an SSH execution environment. ## What Changed - `ssh.ts`: `prepareWorkspaceForSshExecution` lists the project repositories under `.paperclip-repositories/`. It applies the discovery rules of `readGitWorkspaceSnapshot`: each entry must be a directory with a valid name and must be a Git repository root, else the prepare step fails before any transfer. - `ssh.ts`: the anchor copy leaves `.paperclip-repositories/` out. Each project repository then gets the same import, sync, and deleted-path steps as the anchor. The remote anchor repository ignores `/.paperclip-repositories/`, as the local checkout does. - `ssh.ts`: `prepareWorkspaceForSshExecution` returns the transported repositories (the field is present only when there are repositories). `restoreWorkspaceFromSshExecution` accepts them with their baselines. It validates each path and baseline first, then restores the repositories before the anchor and stops at the first failure, as the sandbox restore does. - `remote-managed-runtime.ts`: the anchor baseline excludes `.paperclip-repositories/`, and each project repository gets its own baseline for the restore merge. - `ssh-fixture.test.ts`: regression tests for two consecutive managed runs and for the direct restore path, on a workspace with a project repository (commits, dirty edits, and a deleted file). Two tests for the new validation. - `docs/guides/board-operator/execution-workspaces-and-runtime-services.md`: one line about project repositories in the SSH round trip. ## Verification - The new regression test fails on `master` (`expected 'backend initial\n?? ../\n' to contain 'frontend initial'`) and passes with this change. - `PAPERCLIP_ENABLE_DARWIN_SSH_ENV_LAB=1 npx vitest run packages/adapter-utils/src/ssh-fixture.test.ts packages/adapter-utils/src/remote-managed-runtime.test.ts`: 32 passed, with the sshd fixture running. - `tsc --noEmit` passes for `packages/adapter-utils` and `server`, and `pnpm -r typecheck` passes for the other workspaces. The Rust step of `@paperclipai/paperclip-runner` did not run locally because `cargo` is not installed. - `node ./scripts/check-no-git-push.mjs` and `pnpm check:module-boundaries` pass. - `pnpm test:run` did not complete locally. Before it stopped, 5 tests failed: 2 in `server/src/__tests__/workspace-runtime.test.ts` and 3 in `server/src/__tests__/company-skills-service.test.ts`. The same 5 tests also fail on the base commit `5edf55d73` without this change. CI runs the full suite. - `pnpm build` passes for all workspaces except `@paperclipai/paperclip-runner` and `server`, because their build compiles the Rust runner binary and `cargo` is not installed. `tsc --noEmit` passes for `server`. - Manual test on a self-hosted `v2026.916.1` instance with the same change applied: a project with two repositories and an SSH environment. Two runs on the same task passed. After each run, the second repository keeps its `.git` on the host. On the remote host it is a Git checkout, and the remote anchor ignores it. ## Risks - Low risk. Workspaces without `.paperclip-repositories/` take the same path as before, and the return value is unchanged for them. - A workspace with an invalid entry under `.paperclip-repositories/` now fails the SSH prepare step. The sandbox path already rejects such entries. - If one repository fails to restore, the restore stops, as in the sandbox path. The remote run directory keeps the agent's work. - Each project repository adds one bundle import and one restore per run. The time grows with the number and size of the repositories. - Out of scope: other nested `.git` directories (for example a vendored checkout inside a repository) keep the existing SSH behavior. ## Model Used - Provider and model: Anthropic Claude Opus 5.5 (`claude-opus-5-5`), in Claude Code. - Capabilities: extended thinking, tool use, and code execution. The context window size was not recorded. - Use: the model investigated the bug, wrote the change and the tests, and ran the checks. A separate Claude Code agent reviewed the diff. The author reviewed the change. The manual test ran on the author's self-hosted instance. ## 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
275 lines
9.6 KiB
TypeScript
275 lines
9.6 KiB
TypeScript
import path from "node:path";
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import { GIT_ARCHIVE_EXCLUDES, PROJECT_REPOSITORIES_DIR } from "./git-workspace-sync.js";
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import {
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type SshRemoteExecutionSpec,
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prepareWorkspaceForSshExecution,
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runSshCommand,
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restoreWorkspaceFromSshExecution,
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syncDirectoryToSsh,
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} from "./ssh.js";
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import {
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mergeExcludes,
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referencedSourceIgnoreExcludeEntries,
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type SandboxAdditionalSource,
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type SandboxManagedRuntimeAssetRestoreContext,
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} from "./sandbox-managed-runtime.js";
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import { captureDirectorySnapshot, type DirectorySnapshot } from "./workspace-restore-merge.js";
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import type { RuntimeProgressSink } from "./runtime-progress.js";
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// The fixed heavy-directory excludes every referenced project drops,
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// regardless of its ignore resolution. A `git`-resolved project additionally
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// drops its own resolved ignored paths (see `referencedSourceIgnoreExcludeEntries`
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// and the per-project merge below); an `other` project keeps only this set.
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const REMOTE_ADDITIONAL_SOURCE_HEAVY_DIR_EXCLUDES = [
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"node_modules",
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"vendor",
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"dist",
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"build",
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"out",
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"coverage",
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".next",
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".turbo",
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".cache",
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".git",
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].flatMap((entry) => [entry, `${entry}/*`, `*/${entry}`, `*/${entry}/*`]);
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export interface RemoteManagedRuntimeAsset {
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key: string;
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localDir: string;
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followSymlinks?: boolean;
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exclude?: string[];
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restore?: (ctx: SandboxManagedRuntimeAssetRestoreContext) => Promise<void>;
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}
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export interface PreparedRemoteManagedRuntime {
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spec: SshRemoteExecutionSpec;
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workspaceLocalDir: string;
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workspaceRemoteDir: string;
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runtimeRootDir: string;
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assetDirs: Record<string, string>;
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/**
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* Remote directory of each additional (referenced) project that staged
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* successfully, keyed by `projectId`. A project whose staging failed is
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* absent (per-project failure isolation).
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*/
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additionalSourceDirs: Record<string, string>;
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restoreWorkspace(onProgress?: RuntimeProgressSink): Promise<void>;
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}
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function asObject(value: unknown): Record<string, unknown> {
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return value && typeof value === "object" && !Array.isArray(value)
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? (value as Record<string, unknown>)
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: {};
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}
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function asString(value: unknown): string {
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return typeof value === "string" ? value : "";
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}
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function asNumber(value: unknown): number {
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return typeof value === "number" ? value : Number(value);
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}
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function shellQuote(value: string): string {
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return `'${value.replace(/'/g, `'"'"'`)}'`;
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}
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async function readRemoteFile(spec: SshRemoteExecutionSpec, remotePath: string): Promise<Buffer> {
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const result = await runSshCommand(spec, `base64 < ${shellQuote(remotePath)}`, {
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maxBuffer: 1024 * 1024,
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});
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return Buffer.from(result.stdout.replace(/\s+/g, ""), "base64");
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}
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export function buildRemoteExecutionSessionIdentity(spec: SshRemoteExecutionSpec | null) {
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if (!spec) return null;
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return {
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transport: "ssh",
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host: spec.host,
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port: spec.port,
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username: spec.username,
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remoteCwd: spec.remoteCwd,
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} as const;
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}
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export function remoteExecutionSessionMatches(saved: unknown, current: SshRemoteExecutionSpec | null): boolean {
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const currentIdentity = buildRemoteExecutionSessionIdentity(current);
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if (!currentIdentity) return false;
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const parsedSaved = asObject(saved);
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return (
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asString(parsedSaved.transport) === currentIdentity.transport &&
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asString(parsedSaved.host) === currentIdentity.host &&
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asNumber(parsedSaved.port) === currentIdentity.port &&
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asString(parsedSaved.username) === currentIdentity.username &&
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asString(parsedSaved.remoteCwd) === currentIdentity.remoteCwd
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);
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}
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export async function prepareRemoteManagedRuntime(input: {
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spec: SshRemoteExecutionSpec;
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runId: string;
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adapterKey: string;
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workspaceLocalDir: string;
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workspaceRemoteDir?: string;
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syncWorkspace?: boolean;
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workspaceFileMode?: "all";
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workspaceExclude?: string[];
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assets?: RemoteManagedRuntimeAsset[];
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/** Referenced (additional) projects to stage as plain, read-only trees. */
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additionalSources?: SandboxAdditionalSource[];
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// Upload progress sink. Threaded for the byte-counting transport rewrite; the
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// child task wires it into the workspace/asset transfers.
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onProgress?: RuntimeProgressSink;
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}): Promise<PreparedRemoteManagedRuntime> {
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const baseWorkspaceRemoteDir = input.workspaceRemoteDir ?? input.spec.remoteCwd;
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const syncWorkspace = input.syncWorkspace !== false;
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const workspaceRemoteDir = syncWorkspace
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? path.posix.join(
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baseWorkspaceRemoteDir,
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".paperclip-runtime",
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"runs",
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input.runId,
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"workspace",
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)
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: baseWorkspaceRemoteDir;
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const runtimeRootDir = path.posix.join(workspaceRemoteDir, ".paperclip-runtime", input.adapterKey);
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const preparedWorkspace = syncWorkspace
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? await prepareWorkspaceForSshExecution({
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spec: input.spec,
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localDir: input.workspaceLocalDir,
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remoteDir: workspaceRemoteDir,
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onProgress: input.onProgress,
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workspaceFileMode: input.workspaceFileMode,
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workspaceExclude: input.workspaceExclude,
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})
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: null;
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const projectRepositories = preparedWorkspace?.repositories ?? [];
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const baselineSnapshot = preparedWorkspace
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? await captureDirectorySnapshot(input.workspaceLocalDir, {
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exclude: preparedWorkspace.gitBacked
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? [
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...GIT_ARCHIVE_EXCLUDES,
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".paperclip-runtime",
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...(projectRepositories.length > 0 ? [PROJECT_REPOSITORIES_DIR] : []),
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]
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: [".paperclip-runtime", ...(input.workspaceFileMode === "all" ? input.workspaceExclude ?? [] : [])],
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})
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: null;
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const repositoryBaselines: Array<{ path: string; baselineSnapshot: DirectorySnapshot }> = [];
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for (const repository of projectRepositories) {
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repositoryBaselines.push({
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path: repository,
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baselineSnapshot: await captureDirectorySnapshot(path.join(input.workspaceLocalDir, repository), {
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exclude: [...GIT_ARCHIVE_EXCLUDES, ".paperclip-runtime"],
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}),
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});
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}
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const assetDirs: Record<string, string> = {};
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try {
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for (const asset of input.assets ?? []) {
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const remoteDir = path.posix.join(runtimeRootDir, asset.key);
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assetDirs[asset.key] = remoteDir;
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await syncDirectoryToSsh({
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spec: input.spec,
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localDir: asset.localDir,
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remoteDir,
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followSymlinks: asset.followSymlinks,
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exclude: asset.exclude,
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onProgress: input.onProgress,
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progressLabel: asset.key,
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});
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}
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} catch (error) {
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if (preparedWorkspace && baselineSnapshot) {
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await restoreWorkspaceFromSshExecution({
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spec: input.spec,
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localDir: input.workspaceLocalDir,
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remoteDir: workspaceRemoteDir,
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baselineSnapshot,
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restoreGitHistory: preparedWorkspace.gitBacked,
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onProgress: input.onProgress,
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repositories: repositoryBaselines,
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});
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}
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throw error;
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}
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// Stage each referenced (additional) project as a plain, read-only tree in its
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// OWN isolated remote directory (`project-<projectId>`). Additional sources
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// never get the anchor's git-history/overlay semantics. Per-project failure
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// isolation: one project's failure logs a warning and is skipped; the run and
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// the other projects continue (no workspace restore, unlike an asset failure).
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const additionalSourceDirs: Record<string, string> = {};
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for (const source of input.additionalSources ?? []) {
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const { localPath, projectId, ignoreResolution } = source;
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try {
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if (!path.posix.isAbsolute(localPath)) {
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throw new Error(`additional source localPath is not an absolute path: ${localPath}`);
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}
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if (
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projectId.length === 0 ||
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projectId.includes("/") ||
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projectId.includes("\\") ||
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projectId.includes("..")
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) {
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throw new Error(`additional source projectId is not a simple path segment: ${projectId}`);
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}
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// Fail closed: a project whose ignore resolution failed is not staged at
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// all — the existing per-project skip-and-warn path below handles it.
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if (ignoreResolution.kind === "failed") {
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throw new Error(`referenced project ignore resolution failed: ${ignoreResolution.reason}`);
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}
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const remoteDir = path.posix.join(runtimeRootDir, `project-${projectId}`);
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const exclude = mergeExcludes(
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REMOTE_ADDITIONAL_SOURCE_HEAVY_DIR_EXCLUDES,
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referencedSourceIgnoreExcludeEntries(ignoreResolution),
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);
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await syncDirectoryToSsh({
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spec: input.spec,
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localDir: localPath,
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remoteDir,
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exclude,
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onProgress: input.onProgress,
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progressLabel: `project-${projectId}`,
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});
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additionalSourceDirs[projectId] = remoteDir;
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} catch (error) {
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console.warn(
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`[paperclip] Failed to stage referenced project ${projectId}; skipping it. ${String(error)}`,
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);
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}
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}
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return {
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spec: input.spec,
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workspaceLocalDir: input.workspaceLocalDir,
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workspaceRemoteDir,
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runtimeRootDir,
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assetDirs,
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additionalSourceDirs,
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restoreWorkspace: async (onProgress?: RuntimeProgressSink) => {
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if (preparedWorkspace && baselineSnapshot) {
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await restoreWorkspaceFromSshExecution({
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spec: input.spec,
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localDir: input.workspaceLocalDir,
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remoteDir: workspaceRemoteDir,
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baselineSnapshot,
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restoreGitHistory: preparedWorkspace.gitBacked,
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onProgress,
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repositories: repositoryBaselines,
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});
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}
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for (const asset of input.assets ?? []) {
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if (!asset.restore) continue;
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await asset.restore({
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assetDir: path.posix.join(runtimeRootDir, asset.key),
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readFile: (remotePath) => readRemoteFile(input.spec, remotePath),
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});
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}
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},
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};
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}
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