Harden remote workspace sync and restore flows (#5444)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies
> - When an agent runs against a remote target, Paperclip syncs the
workspace out to the remote at run start and restores changes back to
the local workspace at run end
> - The previous restore flow naïvely overwrote local files with
whatever the remote returned, so files that the remote run never touched
but had timestamp/mode drift could be needlessly rewritten — and a
single static `refs/paperclip/ssh-sync/imported` ref made concurrent SSH
workspace exports race on the same git ref
> - This pull request adds a `workspace-restore-merge` module that diffs
a pre-run snapshot against the post-run remote state and only writes
back files the remote actually changed; SSH workspace exports now use a
per-import unique ref so concurrent runs can't trample each other
> - Every adapter's execute path threads the snapshot through
`prepareAdapterExecutionTargetRuntime` so the merge has the baseline it
needs
> - The benefit is workspace restores no longer churn untouched files,
and concurrent SSH runs no longer collide on the import ref

## What Changed

- `packages/adapter-utils/src/workspace-restore-merge.{ts,test.ts}`: new
module — directory snapshot (kind/mode/sha256/symlink target) plus
snapshot-aware merge that writes only the files the remote changed
- `packages/adapter-utils/src/ssh.ts`: SSH workspace export uses a
per-import unique ref (`refs/paperclip/ssh-sync/imported/<uuid>`);
restore goes through the new merge helper; `ssh-fixture.test.ts` covers
the unique-ref + merge paths
- `packages/adapter-utils/src/sandbox-managed-runtime.ts` +
`remote-managed-runtime.ts`: thread the snapshot/merge through the
sandbox and SSH paths
- `packages/adapter-utils/src/server-utils.{ts,test.ts}` +
`execution-target.ts`: helpers for capturing the pre-run snapshot;
`prepareAdapterExecutionTargetRuntime` gains required `runId` and
optional `workspaceRemoteDir`, and returns the realized
`workspaceRemoteDir`
- Each adapter's `execute.ts` (acpx, claude, codex, cursor, gemini,
opencode, pi) takes the snapshot at run start and passes it through to
the runtime restore
- Remote execute test mocks updated to match the new
`prepareWorkspaceForSshExecution` return shape and the per-run
`${managedRemoteWorkspace}` cwd subdirectory

## Verification

- `pnpm vitest run --no-coverage --project @paperclipai/adapter-utils
--project @paperclipai/adapter-acpx-local --project
@paperclipai/adapter-claude-local --project
@paperclipai/adapter-codex-local --project
@paperclipai/adapter-cursor-local --project
@paperclipai/adapter-gemini-local --project
@paperclipai/adapter-opencode-local --project
@paperclipai/adapter-pi-local` — 196/196 passing
- `pnpm typecheck` clean across the workspace

## Risks

Medium. The restore path now writes a strict subset of what it
previously did — files the remote did not touch are no longer rewritten.
If any flow was relying on a touch-without-content-change being copied
back (timestamp or permission propagation only), that behavior is now
skipped. Snapshot capture adds an O(N-files-in-workspace) hash pass at
run start; the cost is bounded by the existing exclude list. The `runId`
parameter on `prepareAdapterExecutionTargetRuntime` is now required —
every in-tree caller is updated; out-of-tree adapter authors need to
pass it.

## Model Used

Claude Opus 4.7 (1M context)

## 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 run tests locally and they pass
- [x] I have added or updated tests where applicable — new module +
every adapter execute path covered
- [x] If this change affects the UI, I have included before/after
screenshots — N/A (no UI)
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge

packages/adapters/claude-local/src/server/execute.remote.test.ts

@@ -27,7 +27,7 @@ const {
   })),
   ensureCommandResolvable: vi.fn(async () => undefined),
   resolveCommandForLogs: vi.fn(async () => "ssh://fixture@127.0.0.1:2222/remote/workspace :: claude"),
-  prepareWorkspaceForSshExecution: vi.fn(async () => undefined),
+  prepareWorkspaceForSshExecution: vi.fn(async () => ({ gitBacked: false })),
   restoreWorkspaceFromSshExecution: vi.fn(async () => undefined),
   syncDirectoryToSsh: vi.fn(async () => undefined),
   startAdapterExecutionTargetPaperclipBridge: vi.fn(async () => ({
@@ -94,6 +94,7 @@ describe("claude remote execution", () => {
     const workspaceDir = path.join(rootDir, "workspace");
     const alternateWorkspaceDir = path.join(rootDir, "workspace-other");
     const instructionsPath = path.join(rootDir, "instructions.md");
+    const managedRemoteWorkspace = "/remote/workspace/.paperclip-runtime/runs/run-1/workspace";
     await mkdir(workspaceDir, { recursive: true });
     await mkdir(alternateWorkspaceDir, { recursive: true });
     await writeFile(instructionsPath, "Use the remote workspace.\n", "utf8");
@@ -116,6 +117,11 @@ describe("claude remote execution", () => {
       config: {
         command: "claude",
         instructionsFilePath: instructionsPath,
+        env: {
+          QA_PROJECT_WORKSPACE_CWD: workspaceDir,
+          RANDOM_WORKSPACE_CWD: workspaceDir,
+          OTHER_ENV: workspaceDir,
+        },
       },
       context: {
         paperclipWorkspace: {
@@ -161,11 +167,11 @@ describe("claude remote execution", () => {
     expect(prepareWorkspaceForSshExecution).toHaveBeenCalledTimes(1);
     expect(prepareWorkspaceForSshExecution).toHaveBeenCalledWith(expect.objectContaining({
       localDir: workspaceDir,
-      remoteDir: "/remote/workspace",
+      remoteDir: managedRemoteWorkspace,
     }));
     expect(syncDirectoryToSsh).toHaveBeenCalledTimes(1);
     expect(syncDirectoryToSsh).toHaveBeenCalledWith(expect.objectContaining({
-      remoteDir: "/remote/workspace/.paperclip-runtime/claude/skills",
+      remoteDir: `${managedRemoteWorkspace}/.paperclip-runtime/claude/skills`,
       followSymlinks: true,
     }));
     expect(runChildProcess).toHaveBeenCalledTimes(1);
@@ -173,15 +179,17 @@ describe("claude remote execution", () => {
       | [string, string, string[], { env: Record<string, string>; remoteExecution?: { remoteCwd: string } | null }]
       | undefined;
     expect(call?.[2]).toContain("--append-system-prompt-file");
-    expect(call?.[2]).toContain("/remote/workspace/.paperclip-runtime/claude/skills/agent-instructions.md");
+    expect(call?.[2]).toContain(
+      `${managedRemoteWorkspace}/.paperclip-runtime/claude/skills/agent-instructions.md`,
+    );
     expect(call?.[2]).toContain("--add-dir");
-    expect(call?.[2]).toContain("/remote/workspace/.paperclip-runtime/claude/skills");
-    expect(call?.[3].env.PAPERCLIP_WORKSPACE_CWD).toBe("/remote/workspace");
+    expect(call?.[2]).toContain(`${managedRemoteWorkspace}/.paperclip-runtime/claude/skills`);
+    expect(call?.[3].env.PAPERCLIP_WORKSPACE_CWD).toBe(managedRemoteWorkspace);
     expect(call?.[3].env.PAPERCLIP_WORKSPACE_WORKTREE_PATH).toBeUndefined();
     expect(JSON.parse(call?.[3].env.PAPERCLIP_WORKSPACES_JSON ?? "[]")).toEqual([
       {
         workspaceId: "workspace-1",
-        cwd: "/remote/workspace",
+        cwd: managedRemoteWorkspace,
         repoUrl: "https://github.com/paperclipai/paperclip.git",
         repoRef: "main",
       },
@@ -193,12 +201,15 @@ describe("claude remote execution", () => {
     ]);
     expect(call?.[3].env.PAPERCLIP_API_URL).toBe("http://127.0.0.1:4310");
     expect(call?.[3].env.PAPERCLIP_API_BRIDGE_MODE).toBe("queue_v1");
-    expect(call?.[3].remoteExecution?.remoteCwd).toBe("/remote/workspace");
+    expect(call?.[3].env.QA_PROJECT_WORKSPACE_CWD).toBe(managedRemoteWorkspace);
+    expect(call?.[3].env.RANDOM_WORKSPACE_CWD).toBe(managedRemoteWorkspace);
+    expect(call?.[3].env.OTHER_ENV).toBe(workspaceDir);
+    expect(call?.[3].remoteExecution?.remoteCwd).toBe(managedRemoteWorkspace);
     expect(startAdapterExecutionTargetPaperclipBridge).toHaveBeenCalledTimes(1);
     expect(restoreWorkspaceFromSshExecution).toHaveBeenCalledTimes(1);
     expect(restoreWorkspaceFromSshExecution).toHaveBeenCalledWith(expect.objectContaining({
       localDir: workspaceDir,
-      remoteDir: "/remote/workspace",
+      remoteDir: managedRemoteWorkspace,
     }));
   });
 
@@ -259,6 +270,7 @@ describe("claude remote execution", () => {
     const rootDir = await mkdtemp(path.join(os.tmpdir(), "paperclip-claude-remote-resume-match-"));
     cleanupDirs.push(rootDir);
     const workspaceDir = path.join(rootDir, "workspace");
+    const managedRemoteWorkspace = "/remote/workspace/.paperclip-runtime/runs/run-ssh-resume/workspace";
     await mkdir(workspaceDir, { recursive: true });
 
     await execute({
@@ -274,13 +286,13 @@ describe("claude remote execution", () => {
         sessionId: "session-123",
         sessionParams: {
           sessionId: "session-123",
-          cwd: "/remote/workspace",
+          cwd: managedRemoteWorkspace,
           remoteExecution: {
             transport: "ssh",
             host: "127.0.0.1",
             port: 2222,
             username: "fixture",
-            remoteCwd: "/remote/workspace",
+            remoteCwd: managedRemoteWorkspace,
           },
         },
         sessionDisplayId: "session-123",

packages/adapters/claude-local/src/server/execute.ts

@@ -6,6 +6,7 @@ import type { RunProcessResult } from "@paperclipai/adapter-utils/server-utils";
 import {
   adapterExecutionTargetIsRemote,
   adapterExecutionTargetRemoteCwd,
+  overrideAdapterExecutionTargetRemoteCwd,
   adapterExecutionTargetSessionIdentity,
   adapterExecutionTargetSessionMatches,
   adapterExecutionTargetUsesManagedHome,
@@ -35,8 +36,10 @@ import {
   buildInvocationEnvForLogs,
   ensureAbsoluteDirectory,
   ensurePathInEnv,
+  refreshPaperclipWorkspaceEnvForExecution,
   renderTemplate,
   renderPaperclipWakePrompt,
+  rewriteWorkspaceCwdEnvVarsForExecution,
   shapePaperclipWorkspaceEnvForExecution,
   stringifyPaperclipWakePayload,
   DEFAULT_PAPERCLIP_AGENT_PROMPT_TEMPLATE,
@@ -152,7 +155,7 @@ async function buildClaudeRuntimeConfig(input: ClaudeExecutionInput): Promise<Cl
   const effectiveWorkspaceCwd = useConfiguredInsteadOfAgentHome ? "" : workspaceCwd;
   const cwd = effectiveWorkspaceCwd || configuredCwd || process.cwd();
   const executionTargetIsRemote = adapterExecutionTargetIsRemote(executionTarget);
-  const effectiveExecutionCwd = adapterExecutionTargetRemoteCwd(executionTarget, cwd);
+  let effectiveExecutionCwd = adapterExecutionTargetRemoteCwd(executionTarget, cwd);
   const shapedWorkspaceEnv = shapePaperclipWorkspaceEnvForExecution({
     workspaceCwd: effectiveWorkspaceCwd,
     workspaceWorktreePath,
@@ -241,7 +244,13 @@ async function buildClaudeRuntimeConfig(input: ClaudeExecutionInput): Promise<Cl
   if (runtimePrimaryUrl) {
     env.PAPERCLIP_RUNTIME_PRIMARY_URL = runtimePrimaryUrl;
   }
-  for (const [key, value] of Object.entries(envConfig)) {
+  const shapedEnvConfig = rewriteWorkspaceCwdEnvVarsForExecution({
+    env: envConfig,
+    workspaceCwd: effectiveWorkspaceCwd,
+    executionCwd: shapedWorkspaceEnv.workspaceCwd,
+    executionTargetIsRemote,
+  });
+  for (const [key, value] of Object.entries(shapedEnvConfig)) {
     if (typeof value === "string") env[key] = value;
   }
 
@@ -351,6 +360,21 @@ export async function execute(ctx: AdapterExecutionContext): Promise<AdapterExec
   const maxTurns = asNumber(config.maxTurnsPerRun, 0);
   const dangerouslySkipPermissions = asBoolean(config.dangerouslySkipPermissions, true);
   const configEnv = parseObject(config.env);
+  const workspaceContext = parseObject(context.paperclipWorkspace);
+  const workspaceCwd = asString(workspaceContext.cwd, "");
+  const workspaceSource = asString(workspaceContext.source, "");
+  const workspaceStrategy = asString(workspaceContext.strategy, "");
+  const workspaceBranch = asString(workspaceContext.branchName, "") || null;
+  const workspaceWorktreePath = asString(workspaceContext.worktreePath, "") || null;
+  const agentHome = asString(workspaceContext.agentHome, "") || null;
+  const workspaceHints = Array.isArray(context.paperclipWorkspaces)
+    ? context.paperclipWorkspaces.filter(
+        (value): value is Record<string, unknown> => typeof value === "object" && value !== null,
+      )
+    : [];
+  const configuredCwd = asString(config.cwd, "");
+  const useConfiguredInsteadOfAgentHome = workspaceSource === "agent_home" && configuredCwd.length > 0;
+  const effectiveWorkspaceCwd = useConfiguredInsteadOfAgentHome ? "" : workspaceCwd;
   const hasExplicitClaudeConfigDir =
     typeof configEnv.CLAUDE_CONFIG_DIR === "string" && configEnv.CLAUDE_CONFIG_DIR.trim().length > 0;
   const instructionsFilePath = asString(config.instructionsFilePath, "").trim();
@@ -379,7 +403,7 @@ export async function execute(ctx: AdapterExecutionContext): Promise<AdapterExec
     extraArgs,
   } = runtimeConfig;
   let loggedEnv = initialLoggedEnv;
-  const effectiveExecutionCwd = adapterExecutionTargetRemoteCwd(executionTarget, cwd);
+  let effectiveExecutionCwd = adapterExecutionTargetRemoteCwd(executionTarget, cwd);
   const terminalResultCleanupGraceMs = Math.max(
     0,
     asNumber(config.terminalResultCleanupGraceMs, 5_000),
@@ -433,6 +457,7 @@ export async function execute(ctx: AdapterExecutionContext): Promise<AdapterExec
           `[paperclip] Syncing workspace and Claude runtime assets to ${describeAdapterExecutionTarget(executionTarget)}.\n`,
         );
         return await prepareAdapterExecutionTargetRuntime({
+          runId,
           target: executionTarget,
           adapterKey: "claude",
           workspaceLocalDir: cwd,
@@ -455,6 +480,26 @@ export async function execute(ctx: AdapterExecutionContext): Promise<AdapterExec
         });
       })()
     : null;
+  if (preparedExecutionTargetRuntime?.workspaceRemoteDir) {
+    effectiveExecutionCwd = preparedExecutionTargetRuntime.workspaceRemoteDir;
+  }
+  const runtimeExecutionTarget = overrideAdapterExecutionTargetRemoteCwd(executionTarget, effectiveExecutionCwd);
+  refreshPaperclipWorkspaceEnvForExecution({
+    env,
+    envConfig: configEnv,
+    workspaceCwd: effectiveWorkspaceCwd,
+    workspaceSource,
+    workspaceStrategy,
+    workspaceId,
+    workspaceRepoUrl,
+    workspaceRepoRef,
+    workspaceBranch,
+    workspaceWorktreePath,
+    workspaceHints,
+    agentHome,
+    executionTargetIsRemote,
+    executionCwd: effectiveExecutionCwd,
+  });
   const restoreRemoteWorkspace = preparedExecutionTargetRuntime
     ? () => preparedExecutionTargetRuntime.restoreWorkspace()
     : null;
@@ -502,10 +547,10 @@ export async function execute(ctx: AdapterExecutionContext): Promise<AdapterExec
     );
   }
   let paperclipBridge: Awaited<ReturnType<typeof startAdapterExecutionTargetPaperclipBridge>> = null;
-  if (executionTargetIsRemote && adapterExecutionTargetUsesPaperclipBridge(executionTarget)) {
+  if (executionTargetIsRemote && adapterExecutionTargetUsesPaperclipBridge(runtimeExecutionTarget)) {
     paperclipBridge = await startAdapterExecutionTargetPaperclipBridge({
       runId,
-      target: executionTarget,
+      target: runtimeExecutionTarget,
       runtimeRootDir: preparedExecutionTargetRuntime?.runtimeRootDir,
       adapterKey: "claude",
       hostApiToken: env.PAPERCLIP_API_KEY,
@@ -536,7 +581,7 @@ export async function execute(ctx: AdapterExecutionContext): Promise<AdapterExec
     runtimeSessionId.length > 0 &&
     hasMatchingPromptBundle &&
     (runtimeSessionCwd.length === 0 || path.resolve(runtimeSessionCwd) === path.resolve(effectiveExecutionCwd)) &&
-    adapterExecutionTargetSessionMatches(runtimeRemoteExecution, executionTarget);
+    adapterExecutionTargetSessionMatches(runtimeRemoteExecution, runtimeExecutionTarget);
   const sessionId = canResumeSession ? runtimeSessionId : null;
   if (
     executionTargetIsRemote &&
@@ -672,7 +717,7 @@ export async function execute(ctx: AdapterExecutionContext): Promise<AdapterExec
       });
     }
 
-    const proc = await runAdapterExecutionTargetProcess(runId, executionTarget, command, args, {
+    const proc = await runAdapterExecutionTargetProcess(runId, runtimeExecutionTarget, command, args, {
       cwd,
       env,
       stdin: prompt,
@@ -793,7 +838,7 @@ export async function execute(ctx: AdapterExecutionContext): Promise<AdapterExec
         promptBundleKey: promptBundle.bundleKey,
         ...(executionTargetIsRemote
           ? {
-              remoteExecution: adapterExecutionTargetSessionIdentity(executionTarget),
+              remoteExecution: adapterExecutionTargetSessionIdentity(runtimeExecutionTarget),
             }
           : {}),
         ...(workspaceId ? { workspaceId } : {}),