diff --git a/packages/adapter-utils/src/sandbox-managed-runtime.test.ts b/packages/adapter-utils/src/sandbox-managed-runtime.test.ts
index bf5ab10e4df..6b2596f35b9 100644
--- a/packages/adapter-utils/src/sandbox-managed-runtime.test.ts
+++ b/packages/adapter-utils/src/sandbox-managed-runtime.test.ts
@@ -631,6 +631,9 @@ describe("sandbox managed runtime", () => {
     const localAssetsDir = path.join(rootDir, "local-assets");
     const linkedAssetPath = path.join(rootDir, "linked-skill.md");
     await mkdir(path.join(localWorkspaceDir, ".claude"), { recursive: true });
+    const cloneStaging = path.join(".paperclip-runtime", "repository-staging", "pending.clone-abc", "partial.txt");
+    await mkdir(path.dirname(path.join(localWorkspaceDir, cloneStaging)), { recursive: true });
+    await writeFile(path.join(localWorkspaceDir, cloneStaging), "Incomplete private clone");
     await mkdir(localAssetsDir, { recursive: true });
     await writeFile(path.join(localWorkspaceDir, "README.md"), "local workspace\n", "utf8");
     await writeFile(path.join(localWorkspaceDir, "._README.md"), "appledouble\n", "utf8");
@@ -691,6 +694,7 @@ describe("sandbox managed runtime", () => {
     });
 
     await expect(readFile(path.join(remoteWorkspaceDir, "README.md"), "utf8")).resolves.toBe("local workspace\n");
+    await expect(readFile(path.join(remoteWorkspaceDir, cloneStaging), "utf8")).rejects.toMatchObject({ code: "ENOENT" });
     await expect(readFile(path.join(remoteWorkspaceDir, "._README.md"), "utf8")).rejects.toMatchObject({ code: "ENOENT" });
     await expect(readFile(path.join(remoteWorkspaceDir, ".claude", "settings.json"), "utf8")).rejects.toMatchObject({ code: "ENOENT" });
     await expect(readFile(path.join(prepared.assetDirs.skills, "skill.md"), "utf8")).resolves.toBe("skill body\n");
@@ -719,6 +723,7 @@ describe("sandbox managed runtime", () => {
       expect.stringMatching(/^config_sync:Syncing skills to environment: 100% \(\d+\.\d\/\d+\.\d MB\)$/),
       expect.stringMatching(/^restore:Restoring workspace from environment: 100% \(\d+\.\d\/\d+\.\d MB\)$/),
     ]));
+    await expect(readFile(path.join(localWorkspaceDir, cloneStaging), "utf8")).resolves.toBe("Incomplete private clone");
     expect(runtimeStatuses.at(-1)).toBe("finalize:Finalizing workspace");
   });
 
diff --git a/packages/adapter-utils/src/sandbox-managed-runtime.ts b/packages/adapter-utils/src/sandbox-managed-runtime.ts
index 4ee9df6876a..710c237b2cb 100644
--- a/packages/adapter-utils/src/sandbox-managed-runtime.ts
+++ b/packages/adapter-utils/src/sandbox-managed-runtime.ts
@@ -1245,6 +1245,7 @@ export async function prepareSandboxManagedRuntime(input: {
   }
   const gitIgnoredExcludes = directoryIgnore?.kind === "git" ? directoryIgnore.ignoredPaths : undefined;
   const workspaceArchiveExclude = mergeExcludes(
+    [".paperclip-runtime"],
     input.workspaceFileMode === "all" ? [] : SANDBOX_WORKSPACE_HEAVY_DIR_EXCLUDES,
     input.workspaceFileMode === "all" ? [] : [...GIT_ARCHIVE_EXCLUDES],
     input.workspaceExclude,
diff --git a/packages/adapter-utils/src/ssh.ts b/packages/adapter-utils/src/ssh.ts
index 68e61fc6390..ddb07d6ac7b 100644
--- a/packages/adapter-utils/src/ssh.ts
+++ b/packages/adapter-utils/src/ssh.ts
@@ -1090,7 +1090,7 @@ async function isLocalGitRepositoryRoot(localDir: string): Promise<boolean> {
   }
 }
 
-async function listLocalProjectRepositories(localDir: string): Promise<string[]> {
+export async function listLocalProjectRepositories(localDir: string): Promise<string[]> {
   const root = path.join(localDir, PROJECT_REPOSITORIES_DIR);
   const rootStat = await fs.lstat(root).catch((error: NodeJS.ErrnoException) => {
     if (error.code === "ENOENT") return null;
diff --git a/server/src/__tests__/task-workspace-repositories-persistence.test.ts b/server/src/__tests__/task-workspace-repositories-persistence.test.ts
index a84a1f485af..1ca72672573 100644
--- a/server/src/__tests__/task-workspace-repositories-persistence.test.ts
+++ b/server/src/__tests__/task-workspace-repositories-persistence.test.ts
@@ -2,7 +2,7 @@ import { EMBEDDED_POSTGRES_TEST_TIMEOUT_MS } from "@paperclipai/db";
 import { execFile as execFileCallback } from "node:child_process";
 import { promisify } from "node:util";
 import { randomUUID } from "node:crypto";
-import { mkdtemp, rm, mkdir, writeFile, readFile, realpath, open, lstat } from "node:fs/promises";
+import { mkdtemp, rm, mkdir, writeFile, readFile, realpath, open, lstat, symlink, readdir } from "node:fs/promises";
 import { tmpdir } from "node:os";
 import path from "node:path";
 import { constants as fsConstants } from "node:fs";
@@ -11,6 +11,9 @@ import { and, eq } from "drizzle-orm";
 import { agents, companies, createDb, executionWorkspaces, executionWorkspaceRepositories, issues } from "@paperclipai/db";
 import { executionWorkspaceService } from "../services/execution-workspaces.js";
 import { executionWorkspaceRepositoryService } from "../services/execution-workspace-repositories.js";
+import { listLocalProjectRepositories } from "@paperclipai/adapter-utils/ssh";
+import { readManagedWorkspaceRepositories, disposeGitWorkspaceSnapshot } from "@paperclipai/adapter-utils/git-workspace-sync";
+import { captureDirectorySnapshot, disposeDirectorySnapshot } from "@paperclipai/adapter-utils/workspace-restore-merge";
 import { getEmbeddedPostgresTestSupport, startEmbeddedPostgresTestDatabase } from "./helpers/embedded-postgres.js";
 
 const catalog = vi.hoisted(() => ({ available: true }));
@@ -93,6 +96,16 @@ const support = await getEmbeddedPostgresTestSupport();
           new Promise<never>((_, reject) => { timeout = setTimeout(() => reject(new Error("Unrelated repository reuse waited for a blocked clone")), 2000); }),
         ]);
         expect(ready[0]).toMatchObject({ id: readyIntent.operationId, pinnedCommit: pin });
+        // These are the actual SSH and native/sandbox discovery paths while
+        // the unrelated clone is incomplete, not inventory-only assertions.
+        expect(await listLocalProjectRepositories(taskRoot)).toEqual([readyIntent.repository.relativePath]);
+        const snapshots = await readManagedWorkspaceRepositories(taskRoot);
+        try { expect(snapshots.map(repo => repo.path)).toEqual([readyIntent.repository.relativePath]); }
+        finally { await Promise.all(snapshots.map(repo => disposeGitWorkspaceSnapshot(repo.snapshot))); }
+        expect((await readdir(path.join(taskRoot, ".paperclip-runtime", "repository-staging"))).length).toBe(1);
+        const baseline = await captureDirectorySnapshot(taskRoot, { exclude: [".paperclip-runtime"] });
+        try { expect([...baseline.entries.keys()].some(entry => entry.includes("repository-staging") || entry.includes(".clone-"))).toBe(false); }
+        finally { await disposeDirectorySnapshot(baseline); }
       } finally {
         clearTimeout(timeout);
         await writeFile(cloneReleased, "released");
@@ -112,6 +125,23 @@ const support = await getEmbeddedPostgresTestSupport();
       await rm(root, { recursive: true, force: true });
     }
   });
+  it.skipIf(process.platform === "win32")("rejects a symlinked runtime staging parent before cloning", async () => {
+    const root = await mkdtemp(path.join(tmpdir(), "paperclip-unsafe-repository-staging-"));
+    try {
+      const taskRoot = path.join(root, "task"), outside = path.join(root, "outside");
+      await mkdir(taskRoot); await mkdir(outside);
+      await symlink(outside, path.join(taskRoot, ".paperclip-runtime"));
+      const [workspace] = await db.insert(executionWorkspaces).values({ companyId, name: "Unsafe staging", cwd: taskRoot,
+        mode: "shared_workspace", strategyType: "task_directory" }).returning();
+      const [task] = await db.insert(issues).values({ companyId, title: "Unsafe staging", executionWorkspaceId: workspace.id }).returning();
+      await executionWorkspaceRepositoryService(db).request({ companyId, issueId: task.id, actor,
+        request: { repository: { kind: "catalog", id: "123" }, requestKey: "unsafe-staging" } });
+      await expect(executionWorkspaceRepositoryService(db).prepareForAdmission({ companyId, issueId: task.id,
+        workspaceId: workspace.id, cwd: taskRoot, agentId, runId: randomUUID(), responsibleUserId: "local-board" }))
+        .rejects.toThrow("staging directory escapes");
+      expect(await readdir(outside)).toEqual([]);
+    } finally { await rm(root, { recursive: true, force: true }); }
+  });
   it("converges concurrent requests and persists each retry key without creating a project", async () => {
     const [peerIssue] = await db.insert(issues).values({ companyId, title: "Peer task sharing the root", executionWorkspaceId: workspaceId }).returning();
     await db.update(executionWorkspaces).set({ sourceIssueId: issueId }).where(eq(executionWorkspaces.id, workspaceId));
diff --git a/server/src/services/execution-workspace-repositories.ts b/server/src/services/execution-workspace-repositories.ts
index 73d1acc58c0..87416e73b6e 100644
--- a/server/src/services/execution-workspace-repositories.ts
+++ b/server/src/services/execution-workspace-repositories.ts
@@ -129,6 +129,19 @@ export function executionWorkspaceRepositoryService(db: Db) {
     const repositoryRoot = path.join(root, ".paperclip-repositories");
     await fs.mkdir(repositoryRoot, { recursive: true });
     if ((await fs.lstat(repositoryRoot)).isSymbolicLink() || await fs.realpath(repositoryRoot) !== repositoryRoot) throw conflict("Repository directory escapes the task workspace");
+    // Incomplete clones belong to the runtime tree, which is excluded from
+    // transfer and recovery. The published namespace contains checkouts only.
+    let stagingParent = root;
+    for (const name of [".paperclip-runtime", "repository-staging"]) {
+      stagingParent = path.join(stagingParent, name);
+      await fs.mkdir(stagingParent, { mode: 0o700 }).catch((error: NodeJS.ErrnoException) => {
+        if (error.code !== "EEXIST") throw error;
+      });
+      const entry = await fs.lstat(stagingParent);
+      if (!entry.isDirectory() || entry.isSymbolicLink() || await fs.realpath(stagingParent) !== stagingParent) {
+        throw conflict("Repository staging directory escapes the task workspace");
+      }
+    }
     await ensureManagedRepositoriesIgnored(root);
     const prepared: Array<{ id: string; cwd: string; repoUrl: string; relativePath: string; pinnedCommit: string; branchName: string | null }> = [];
     for (const row of rows) {
@@ -167,6 +180,7 @@ export function executionWorkspaceRepositoryService(db: Db) {
           }
           const result = await materializeManagedProjectWorkspace(cwd, {
             repoUrl: row.repoUrl,
+            stagingParent,
             repoRef: authorizedPin ?? (row.requestedRef === "HEAD" ? null : row.requestedRef),
             resolveGitAuth: source.catalogRepositoryId ? resolveAuth : async () => anonymous,
             beforePublish: async cloneCwd => {
diff --git a/server/src/services/managed-repository-checkout.ts b/server/src/services/managed-repository-checkout.ts
index 49919bfde0d..e758479b348 100644
--- a/server/src/services/managed-repository-checkout.ts
+++ b/server/src/services/managed-repository-checkout.ts
@@ -22,6 +22,8 @@ export async function materializeManagedProjectWorkspace(
     resolveGitAuth?: GitRemoteAuthProvider | null;
     /** Internal preparation receipt is committed inside the clone before atomic publication. */
     beforePublish?: (cloneCwd: string) => Promise<void>;
+    /** Existing, validated private staging parent outside published repositories. */
+    stagingParent?: string;
   },
 ): Promise<{ cwd: string; warning: string | null }> {
   await fs.mkdir(path.dirname(cwd), { recursive: true });
@@ -54,14 +56,16 @@ export async function materializeManagedProjectWorkspace(
     await fs.rm(cwd, { recursive: true, force: true });
   }
 
-  // Clone into a temp sibling, then move into place atomically. The shared target directory
+  // Clone into a private temp directory (a sibling by default), then publish atomically. The target
   // is never created in a partial state and never removed on failure, so a concurrent
   // materialization (another process, or a run racing this one) can neither adopt a broken
   // checkout nor lose its own completed one.
   const auth = input.resolveGitAuth && !input.localSource
     ? await input.resolveGitAuth(input.repoUrl)
     : null;
-  const cloneTmpDir = await fs.mkdtemp(`${cwd}.clone-`);
+  const cloneTmpDir = await fs.mkdtemp(input.stagingParent
+    ? path.join(input.stagingParent, `${path.basename(cwd)}.clone-`)
+    : `${cwd}.clone-`);
   try {
     try {
       await execFile(