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/gemini-local/src/server/execute.remote.test.ts

@@ -33,7 +33,7 @@ const {
   })),
   ensureCommandResolvable: vi.fn(async () => undefined),
   resolveCommandForLogs: vi.fn(async () => "ssh://fixture@127.0.0.1:2222/remote/workspace :: gemini"),
-  prepareWorkspaceForSshExecution: vi.fn(async () => undefined),
+  prepareWorkspaceForSshExecution: vi.fn(async () => ({ gitBacked: false })),
   restoreWorkspaceFromSshExecution: vi.fn(async () => undefined),
   runSshCommand: vi.fn(async () => ({
     stdout: "/home/agent",
@@ -105,6 +105,7 @@ describe("gemini remote execution", () => {
     cleanupDirs.push(rootDir);
     const workspaceDir = path.join(rootDir, "workspace");
     const alternateWorkspaceDir = path.join(rootDir, "workspace-other");
+    const managedRemoteWorkspace = "/remote/workspace/.paperclip-runtime/runs/run-1/workspace";
     await mkdir(workspaceDir, { recursive: true });
     await mkdir(alternateWorkspaceDir, { recursive: true });
 
@@ -163,19 +164,19 @@ describe("gemini remote execution", () => {
 
     expect(result.sessionParams).toMatchObject({
       sessionId: "gemini-session-1",
-      cwd: "/remote/workspace",
+      cwd: managedRemoteWorkspace,
       remoteExecution: {
         transport: "ssh",
         host: "127.0.0.1",
         port: 2222,
         username: "fixture",
-        remoteCwd: "/remote/workspace",
+        remoteCwd: managedRemoteWorkspace,
       },
     });
     expect(prepareWorkspaceForSshExecution).toHaveBeenCalledTimes(1);
     expect(syncDirectoryToSsh).toHaveBeenCalledTimes(1);
     expect(syncDirectoryToSsh).toHaveBeenCalledWith(expect.objectContaining({
-      remoteDir: "/remote/workspace/.paperclip-runtime/gemini/skills",
+      remoteDir: `${managedRemoteWorkspace}/.paperclip-runtime/gemini/skills`,
       followSymlinks: true,
     }));
     expect(runSshCommand).toHaveBeenCalledWith(
@@ -186,11 +187,11 @@ describe("gemini remote execution", () => {
     const call = runChildProcess.mock.calls[0] as unknown as
       | [string, string, string[], { env: Record<string, string>; remoteExecution?: { remoteCwd: string } | null }]
       | undefined;
-    expect(call?.[3].env.PAPERCLIP_WORKSPACE_CWD).toBe("/remote/workspace");
+    expect(call?.[3].env.PAPERCLIP_WORKSPACE_CWD).toBe(managedRemoteWorkspace);
     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",
       },
@@ -202,7 +203,7 @@ describe("gemini 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].remoteExecution?.remoteCwd).toBe(managedRemoteWorkspace);
     expect(startAdapterExecutionTargetPaperclipBridge).toHaveBeenCalledTimes(1);
     expect(restoreWorkspaceFromSshExecution).toHaveBeenCalledTimes(1);
   });
@@ -211,6 +212,7 @@ describe("gemini remote execution", () => {
     const rootDir = await mkdtemp(path.join(os.tmpdir(), "paperclip-gemini-remote-resume-"));
     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({
@@ -226,13 +228,13 @@ describe("gemini 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/gemini-local/src/server/execute.ts

@@ -7,6 +7,7 @@ import type { AdapterExecutionContext, AdapterExecutionResult } from "@paperclip
 import {
   adapterExecutionTargetIsRemote,
   adapterExecutionTargetRemoteCwd,
+  overrideAdapterExecutionTargetRemoteCwd,
   adapterExecutionTargetSessionIdentity,
   adapterExecutionTargetSessionMatches,
   adapterExecutionTargetUsesManagedHome,
@@ -27,13 +28,13 @@ import {
   asNumber,
   asString,
   asStringArray,
-  applyPaperclipWorkspaceEnv,
   buildPaperclipEnv,
   buildInvocationEnvForLogs,
   ensureAbsoluteDirectory,
   ensurePaperclipSkillSymlink,
   joinPromptSections,
   ensurePathInEnv,
+  refreshPaperclipWorkspaceEnvForExecution,
   readPaperclipRuntimeSkillEntries,
   readPaperclipIssueWorkModeFromContext,
   resolvePaperclipDesiredSkillNames,
@@ -41,7 +42,6 @@ import {
   parseObject,
   renderTemplate,
   renderPaperclipWakePrompt,
-  shapePaperclipWorkspaceEnvForExecution,
   stringifyPaperclipWakePayload,
   DEFAULT_PAPERCLIP_AGENT_PROMPT_TEMPLATE,
   runChildProcess,
@@ -202,13 +202,7 @@ export async function execute(ctx: AdapterExecutionContext): Promise<AdapterExec
   const useConfiguredInsteadOfAgentHome = workspaceSource === "agent_home" && configuredCwd.length > 0;
   const effectiveWorkspaceCwd = useConfiguredInsteadOfAgentHome ? "" : workspaceCwd;
   const cwd = effectiveWorkspaceCwd || configuredCwd || process.cwd();
-  const effectiveExecutionCwd = adapterExecutionTargetRemoteCwd(executionTarget, cwd);
-  const shapedWorkspaceEnv = shapePaperclipWorkspaceEnvForExecution({
-    workspaceCwd: effectiveWorkspaceCwd,
-    workspaceHints,
-    executionTargetIsRemote,
-    executionCwd: effectiveExecutionCwd,
-  });
+  let effectiveExecutionCwd = adapterExecutionTargetRemoteCwd(executionTarget, cwd);
   await ensureAbsoluteDirectory(cwd, { createIfMissing: true });
   const geminiSkillEntries = await readPaperclipRuntimeSkillEntries(config, __moduleDir);
   const desiredGeminiSkillNames = resolvePaperclipDesiredSkillNames(config, geminiSkillEntries);
@@ -254,20 +248,19 @@ export async function execute(ctx: AdapterExecutionContext): Promise<AdapterExec
   if (approvalStatus) env.PAPERCLIP_APPROVAL_STATUS = approvalStatus;
   if (linkedIssueIds.length > 0) env.PAPERCLIP_LINKED_ISSUE_IDS = linkedIssueIds.join(",");
   if (wakePayloadJson) env.PAPERCLIP_WAKE_PAYLOAD_JSON = wakePayloadJson;
-  applyPaperclipWorkspaceEnv(env, {
-    workspaceCwd: shapedWorkspaceEnv.workspaceCwd,
+  refreshPaperclipWorkspaceEnvForExecution({
+    env,
+    envConfig,
+    workspaceCwd: effectiveWorkspaceCwd,
     workspaceSource,
     workspaceId,
     workspaceRepoUrl,
     workspaceRepoRef,
+    workspaceHints,
     agentHome,
+    executionTargetIsRemote,
+    executionCwd: effectiveExecutionCwd,
   });
-  if (shapedWorkspaceEnv.workspaceHints.length > 0) {
-    env.PAPERCLIP_WORKSPACES_JSON = JSON.stringify(shapedWorkspaceEnv.workspaceHints);
-  }
-  for (const [key, value] of Object.entries(envConfig)) {
-    if (typeof value === "string") env[key] = value;
-  }
   if (!hasExplicitApiKey && authToken) {
     env.PAPERCLIP_API_KEY = authToken;
   }
@@ -322,6 +315,7 @@ export async function execute(ctx: AdapterExecutionContext): Promise<AdapterExec
         `[paperclip] Syncing workspace and Gemini runtime assets to ${describeAdapterExecutionTarget(executionTarget)}.\n`,
       );
       const preparedExecutionTargetRuntime = await prepareAdapterExecutionTargetRuntime({
+        runId,
         target: executionTarget,
         adapterKey: "gemini",
         workspaceLocalDir: cwd,
@@ -334,6 +328,20 @@ export async function execute(ctx: AdapterExecutionContext): Promise<AdapterExec
         }],
       });
       restoreRemoteWorkspace = () => preparedExecutionTargetRuntime.restoreWorkspace();
+      effectiveExecutionCwd = preparedExecutionTargetRuntime.workspaceRemoteDir ?? effectiveExecutionCwd;
+      refreshPaperclipWorkspaceEnvForExecution({
+        env,
+        envConfig,
+        workspaceCwd: effectiveWorkspaceCwd,
+        workspaceSource,
+        workspaceId,
+        workspaceRepoUrl,
+        workspaceRepoRef,
+        workspaceHints,
+        agentHome,
+        executionTargetIsRemote,
+        executionCwd: effectiveExecutionCwd,
+      });
       remoteRuntimeRootDir = preparedExecutionTargetRuntime.runtimeRootDir;
       const managedHome = adapterExecutionTargetUsesManagedHome(executionTarget);
       if (managedHome && preparedExecutionTargetRuntime.runtimeRootDir) {
@@ -366,9 +374,10 @@ export async function execute(ctx: AdapterExecutionContext): Promise<AdapterExec
     }
   }
   if (executionTargetIsRemote && adapterExecutionTargetUsesPaperclipBridge(executionTarget)) {
+    const runtimeExecutionTarget = overrideAdapterExecutionTargetRemoteCwd(executionTarget, effectiveExecutionCwd);
     paperclipBridge = await startAdapterExecutionTargetPaperclipBridge({
       runId,
-      target: executionTarget,
+      target: runtimeExecutionTarget,
       runtimeRootDir: remoteRuntimeRootDir,
       adapterKey: "gemini",
       hostApiToken: env.PAPERCLIP_API_KEY,
@@ -383,6 +392,7 @@ export async function execute(ctx: AdapterExecutionContext): Promise<AdapterExec
       });
     }
   }
+  const runtimeExecutionTarget = overrideAdapterExecutionTargetRemoteCwd(executionTarget, effectiveExecutionCwd);
 
   const runtimeSessionParams = parseObject(runtime.sessionParams);
   const runtimeSessionId = asString(runtimeSessionParams.sessionId, runtime.sessionId ?? "");
@@ -391,7 +401,7 @@ export async function execute(ctx: AdapterExecutionContext): Promise<AdapterExec
   const canResumeSession =
     runtimeSessionId.length > 0 &&
     (runtimeSessionCwd.length === 0 || path.resolve(runtimeSessionCwd) === path.resolve(effectiveExecutionCwd)) &&
-    adapterExecutionTargetSessionMatches(runtimeRemoteExecution, executionTarget);
+    adapterExecutionTargetSessionMatches(runtimeRemoteExecution, runtimeExecutionTarget);
   const sessionId = canResumeSession ? runtimeSessionId : null;
   if (executionTargetIsRemote && runtimeSessionId && !canResumeSession) {
     await onLog(
@@ -512,7 +522,7 @@ 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,
       timeoutSec,
@@ -586,7 +596,7 @@ export async function execute(ctx: AdapterExecutionContext): Promise<AdapterExec
         ...(workspaceRepoRef ? { repoRef: workspaceRepoRef } : {}),
         ...(executionTargetIsRemote
           ? {
-              remoteExecution: adapterExecutionTargetSessionIdentity(executionTarget),
+              remoteExecution: adapterExecutionTargetSessionIdentity(runtimeExecutionTarget),
             }
           : {}),
       } as Record<string, unknown>)