fix(uploads): persist thread uploads canonically and fail fast on upload errors (#943)

* fix(uploads): persist thread uploads canonically and fail fast on upload errors

 - write uploads to thread-scoped storage first to guarantee agent visibility
 - sync files to sandbox virtual path only for non-local sandboxes
 - fix markdown conversion flow to operate on canonical saved files and sync converted files when needed
 - prevent silent attachment upload failures in frontend submit flow (show error + abort submit)
 - add regression tests for local vs non-local upload behavior
 - update upload docs with thread-first persistence and troubleshooting notes

* Update frontend/src/core/threads/hooks.ts

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* fix(uploads): reject "." and ".." filenames in upload sanitization (#944)

* Initial plan

* fix(uploads): reject '.' and '..' filenames in upload sanitization

Co-authored-by: WillemJiang <219644+WillemJiang@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: WillemJiang <219644+WillemJiang@users.noreply.github.com>
Co-authored-by: Willem Jiang <willem.jiang@gmail.com>

---------

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>

backend/tests/test_uploads_router.py

@@ -0,0 +1,100 @@
+import asyncio
+from io import BytesIO
+from pathlib import Path
+from unittest.mock import AsyncMock, MagicMock, patch
+
+from fastapi import UploadFile
+
+from src.gateway.routers import uploads
+
+
+def test_upload_files_writes_thread_storage_and_skips_local_sandbox_sync(tmp_path):
+    thread_uploads_dir = tmp_path / "uploads"
+    thread_uploads_dir.mkdir(parents=True)
+
+    provider = MagicMock()
+    provider.acquire.return_value = "local"
+    sandbox = MagicMock()
+    provider.get.return_value = sandbox
+
+    with (
+        patch.object(uploads, "get_uploads_dir", return_value=thread_uploads_dir),
+        patch.object(uploads, "get_sandbox_provider", return_value=provider),
+    ):
+
+        file = UploadFile(filename="notes.txt", file=BytesIO(b"hello uploads"))
+        result = asyncio.run(uploads.upload_files("thread-local", files=[file]))
+
+    assert result.success is True
+    assert len(result.files) == 1
+    assert result.files[0]["filename"] == "notes.txt"
+    assert (thread_uploads_dir / "notes.txt").read_bytes() == b"hello uploads"
+
+    sandbox.update_file.assert_not_called()
+
+
+def test_upload_files_syncs_non_local_sandbox_and_marks_markdown_file(tmp_path):
+    thread_uploads_dir = tmp_path / "uploads"
+    thread_uploads_dir.mkdir(parents=True)
+
+    provider = MagicMock()
+    provider.acquire.return_value = "aio-1"
+    sandbox = MagicMock()
+    provider.get.return_value = sandbox
+
+    async def fake_convert(file_path: Path) -> Path:
+        md_path = file_path.with_suffix(".md")
+        md_path.write_text("converted", encoding="utf-8")
+        return md_path
+
+    with (
+        patch.object(uploads, "get_uploads_dir", return_value=thread_uploads_dir),
+        patch.object(uploads, "get_sandbox_provider", return_value=provider),
+        patch.object(uploads, "convert_file_to_markdown", AsyncMock(side_effect=fake_convert)),
+    ):
+
+        file = UploadFile(filename="report.pdf", file=BytesIO(b"pdf-bytes"))
+        result = asyncio.run(uploads.upload_files("thread-aio", files=[file]))
+
+    assert result.success is True
+    assert len(result.files) == 1
+    file_info = result.files[0]
+    assert file_info["filename"] == "report.pdf"
+    assert file_info["markdown_file"] == "report.md"
+
+    assert (thread_uploads_dir / "report.pdf").read_bytes() == b"pdf-bytes"
+    assert (thread_uploads_dir / "report.md").read_text(encoding="utf-8") == "converted"
+
+    sandbox.update_file.assert_any_call("/mnt/user-data/uploads/report.pdf", b"pdf-bytes")
+    sandbox.update_file.assert_any_call("/mnt/user-data/uploads/report.md", b"converted")
+
+
+def test_upload_files_rejects_dotdot_and_dot_filenames(tmp_path):
+    thread_uploads_dir = tmp_path / "uploads"
+    thread_uploads_dir.mkdir(parents=True)
+
+    provider = MagicMock()
+    provider.acquire.return_value = "local"
+    sandbox = MagicMock()
+    provider.get.return_value = sandbox
+
+    with (
+        patch.object(uploads, "get_uploads_dir", return_value=thread_uploads_dir),
+        patch.object(uploads, "get_sandbox_provider", return_value=provider),
+    ):
+        # These filenames must be rejected outright
+        for bad_name in ["..", "."]:
+            file = UploadFile(filename=bad_name, file=BytesIO(b"data"))
+            result = asyncio.run(uploads.upload_files("thread-local", files=[file]))
+            assert result.success is True
+            assert result.files == [], f"Expected no files for unsafe filename {bad_name!r}"
+
+        # Path-traversal prefixes are stripped to the basename and accepted safely
+        file = UploadFile(filename="../etc/passwd", file=BytesIO(b"data"))
+        result = asyncio.run(uploads.upload_files("thread-local", files=[file]))
+        assert result.success is True
+        assert len(result.files) == 1
+        assert result.files[0]["filename"] == "passwd"
+
+    # Only the safely normalised file should exist
+    assert [f.name for f in thread_uploads_dir.iterdir()] == ["passwd"]