Add atomic .part staging + runtime download root tools

Atomic write pattern (tier-3 polish from headless test finding):
- download_to_file now writes to <dest>.part and renames to <dest> only on
  successful stream completion (os.replace is POSIX-atomic). Failed
  downloads leave only the .part file — no misleading 0-byte dest files
  in the user's downloads directory.
- Resume logic reads from <dest>.part instead of <dest>; the user's
  directory only ever contains complete files or clearly-marked .part files.
- New `already_complete` short-circuit: if dest exists and no .part, skip
  the network entirely (still re-verify MD5 if requested). The headless
  Claude test confirmed this avoids redundant CDN load.
- Symlink rejection re-added at the new code path: even though os.replace
  would only replace (not follow) a symlink at dest, predictable refusal
  beats silent symlink removal.

Runtime download root tools (for stdio MCP mode):
- get_download_root(): reports current root, source (env var vs default),
  existence, writability.
- set_download_root(path): change MCARCHIVE_DOWNLOAD_ROOT mid-session.
  Expands ~, creates the dir, refuses system paths
  (/, /etc, /usr, /bin, /sbin, /var, /sys, /proc, /dev, /boot, /root).
  The lazy-resolved root means the change takes effect on the next
  download_file call without restarting the server.

14 new tests (66 total, all green, ruff clean):
- 4 staging tests: failed download leaves no dest, success leaves no .part,
  already_complete short-circuit, MD5 verification on existing files
- 6 root-tools tests: env reporting, default reporting, ~ expansion,
  system-dir refusal (parametrized), set→download takes effect immediately
- 4 existing tests rewritten to use .part as the resume staging file

Headless Claude smoke test verified end-to-end: get_download_root →
set_download_root → search → list → download → second download
short-circuits with already_complete=true and zero network bytes.

src/mcarchive_org/client.py

@@ -329,11 +329,21 @@ class ArchiveClient:
         verify_md5: str | None = None,
         chunk_cb=None,
     ) -> dict[str, Any]:
-        """Download with resume support. Returns stats + md5 verification result.
+        """Download with resume support, atomically promoted on success.
 
-        Caller is responsible for ensuring `dest` is confined to a safe directory
+        Writes go to a `<dest>.part` staging file. On success, that staging file
-        (use mcarchive_org.server's path validation, or do your own). This method
+        is atomically renamed to `dest` (POSIX rename is observed all-or-nothing).
-        adds defense-in-depth via O_NOFOLLOW but does not validate path confinement.
+        On any failure, the `.part` file remains and a follow-up call resumes
+        from it — meaning the user's directory only ever contains complete files
+        or `.part` files (which clearly signal incomplete state).
+
+        - `dest` already complete (no .part) and overwrite implied false →
+          early-return with `already_complete: True` (still verifies MD5 if asked).
+        - `.part` exists → resume from its size, append, then promote on success.
+        - Neither exists → fresh download to `.part`, promote on success.
+
+        Caller is responsible for path confinement; this method adds O_NOFOLLOW
+        defense-in-depth but does not enforce a download root.
         """
         validate_identifier(identifier)
         validate_filename(filename)
@@ -343,19 +353,50 @@ class ArchiveClient:
         # check should already have caught this, but redundant defense is cheap.
         if dest.parent.is_symlink():
             raise ArchiveError(f"refusing to write into symlinked directory: {dest.parent}")
+        # Refuse to "download over" a symlink at dest. Even though the staging
+        # rename would replace (not follow) the symlink, predictable refusal is
+        # better than silent symlink removal — that surprises the user and could
+        # destroy a symlink farm they intentionally set up.
+        if dest.is_symlink():
+            raise ArchiveError(f"refusing to write through symlink at {dest}")
 
-        resume_from = dest.stat().st_size if dest.exists() and not dest.is_symlink() else 0
+        part = dest.with_name(dest.name + ".part")
-        # is_symlink() detection: if dest is a symlink, treat as fresh (open with
+        # Same protection on the staging path.
-        # O_NOFOLLOW will refuse anyway, so we won't actually corrupt the target).
+        if part.is_symlink():
+            raise ArchiveError(f"refusing to write through symlink at {part}")
+
+        # Short-circuit: dest already exists complete and no .part to resume.
+        if dest.exists() and not dest.is_symlink() and not part.exists():
+            size = dest.stat().st_size
+            result: dict[str, Any] = {
+                "path": str(dest),
+                "bytes_written": size,
+                "resumed_from": size,
+                "already_complete": True,
+            }
+            if verify_md5:
+                # Verify the existing file matches the expected hash.
+                hasher = hashlib.md5()
+                with dest.open("rb") as fh:
+                    while chunk := fh.read(1 << 16):
+                        hasher.update(chunk)
+                actual = hasher.hexdigest()
+                result["md5_actual"] = actual
+                result["md5_expected"] = verify_md5
+                result["md5_ok"] = actual.lower() == verify_md5.lower()
+            return result
+
+        # Resume from .part if present; otherwise fresh.
+        resume_from = part.stat().st_size if part.exists() and not part.is_symlink() else 0
 
         hasher = hashlib.md5() if verify_md5 else None
         if hasher and resume_from:
-            with dest.open("rb") as f:
+            with part.open("rb") as fh:
-                while chunk := f.read(1 << 16):
+                while chunk := fh.read(1 << 16):
                     hasher.update(chunk)
 
         bytes_written = resume_from
-        f = _safe_open_for_write(dest, append=resume_from > 0)
+        f = _safe_open_for_write(part, append=resume_from > 0)
         try:
             async for chunk in self.stream_file(identifier, filename, resume_from=resume_from):
                 f.write(chunk)
@@ -365,22 +406,24 @@ class ArchiveClient:
                 if chunk_cb:
                     chunk_cb(bytes_written)
         except (httpx.ReadError, httpx.RemoteProtocolError, httpx.ConnectError, httpx.ReadTimeout) as e:
-            # H1: surface partial-state context so the caller can decide whether
+            # H1: surface partial-state context. The .part file stays on disk
-            # to resume or restart. The bytes already on disk are valid (we only
+            # so a follow-up call with overwrite=False resumes from bytes_written.
-            # write whole chunks), so a follow-up call with overwrite=False will
-            # resume cleanly from `bytes_written`.
             raise ArchiveError(
                 f"download interrupted after {bytes_written - resume_from} new bytes "
-                f"({bytes_written} total on disk, resumed from {resume_from}). "
+                f"({bytes_written} total in {part.name}, resumed from {resume_from}). "
-                f"File at {dest} — call download_file again to resume. Cause: {e!r}"
+                f"Call download_file again to resume. Cause: {e!r}"
             ) from e
         finally:
             f.close()
 
-        result: dict[str, Any] = {
+        # Atomic promotion — only after the stream completed cleanly.
+        os.replace(part, dest)
+
+        result = {
             "path": str(dest),
             "bytes_written": bytes_written,
             "resumed_from": resume_from,
+            "already_complete": False,
         }
         if verify_md5 and hasher:
             actual = hasher.hexdigest()

src/mcarchive_org/server.py

@@ -342,13 +342,18 @@ async def download_file(
     so two parallel tool invocations can't race on the same destination file.
     """
     dest = _confine_dest(identifier, filename, dest_dir)
+    part = dest.with_name(dest.name + ".part")
 
     lock = _download_lock_for(identifier, filename)
     async with lock:
-        if overwrite and (dest.exists() or dest.is_symlink()):
+        if overwrite:
-            # is_symlink() before exists() — a dangling symlink reports exists()=False
+            # Remove both the final file AND any leftover .part — we want to start
-            # but we still want to remove the link itself rather than follow it.
+            # truly fresh, not resume an old partial. is_symlink check first since
+            # a dangling symlink reports exists()=False.
+            if dest.exists() or dest.is_symlink():
                 dest.unlink()
+            if part.exists() or part.is_symlink():
+                part.unlink()
 
         try:
             c = await get_shared_client()
@@ -363,6 +368,76 @@ async def download_file(
     return result
 
 
+# ---------- runtime configuration ----------
+
+# Paths we refuse to use as a download root no matter what — these are system
+# directories where writing junk is genuinely harmful. The user's MCP client
+# can usually re-launch with MCARCHIVE_DOWNLOAD_ROOT pointing anywhere they
+# want at startup; this guard is just for the LLM-driven set_download_root tool.
+_FORBIDDEN_ROOTS = frozenset({
+    "/", "/etc", "/usr", "/bin", "/sbin", "/var", "/sys", "/proc", "/dev", "/boot", "/root",
+})
+
+
+def _check_root_safety(p: Path) -> None:
+    s = str(p)
+    if s in _FORBIDDEN_ROOTS:
+        raise ValueError(f"refusing to use system directory as download root: {s}")
+    for forbidden in _FORBIDDEN_ROOTS:
+        if forbidden != "/" and s.startswith(forbidden + "/"):
+            raise ValueError(f"refusing to use system directory as download root: {s}")
+
+
+@mcp.tool
+def get_download_root() -> dict[str, Any]:
+    """Report the directory where download_file writes by default.
+
+    Useful at the start of a session to confirm where files will land. The
+    `source` field tells you whether the value came from the MCARCHIVE_DOWNLOAD_ROOT
+    env var or from the built-in default of `./downloads` under the server's CWD.
+    """
+    raw_env = os.environ.get("MCARCHIVE_DOWNLOAD_ROOT")
+    root = _resolve_download_root().resolve()
+    return {
+        "download_root": str(root),
+        "exists": root.exists(),
+        "writable": os.access(root, os.W_OK) if root.exists() else None,
+        "source": "MCARCHIVE_DOWNLOAD_ROOT env var" if raw_env else "default (./downloads under server CWD)",
+        "raw_env_value": raw_env,
+    }
+
+
+@mcp.tool
+def set_download_root(
+    path: Annotated[
+        str,
+        Field(description="New download root path. '~' is expanded; the directory is created if missing."),
+    ],
+) -> dict[str, Any]:
+    """Change the download root for the rest of this MCP server session.
+
+    Useful when running as a stdio MCP server, since you can't otherwise
+    re-export environment variables to a running child process. The change
+    persists until the server process exits or set_download_root is called
+    again. System directories (/etc, /usr, /var, /sys, /proc, /dev, /boot,
+    /root, /bin, /sbin, /) are refused.
+    """
+    expanded = Path(path).expanduser().resolve()
+    _check_root_safety(expanded)
+
+    previous = _resolve_download_root().resolve()
+    expanded.mkdir(parents=True, exist_ok=True)
+    if not os.access(expanded, os.W_OK):
+        raise ValueError(f"download root not writable: {expanded}")
+
+    os.environ["MCARCHIVE_DOWNLOAD_ROOT"] = str(expanded)
+    return {
+        "download_root": str(expanded),
+        "previous": str(previous),
+        "changed": str(expanded) != str(previous),
+    }
+
+
 # ---------- resources ----------
 
 

tests/test_client_mocked.py

@@ -102,7 +102,8 @@ async def test_resume_with_200_response_raises_before_writing(tmp_path):
     """If the server returns 200 instead of 206 on a Range request, we must not
     append to the existing file — that path corrupts data silently."""
     dest = tmp_path / "partial.bin"
-    dest.write_bytes(b"X" * 100)  # pretend we have a partial download
+    part = tmp_path / "partial.bin.part"  # staging file holds resume state
+    part.write_bytes(b"X" * 100)
 
     def handler(req: httpx.Request) -> httpx.Response:
         # Server ignores Range header and returns the full body with 200
@@ -113,14 +114,16 @@ async def test_resume_with_200_response_raises_before_writing(tmp_path):
         with pytest.raises(ArchiveError, match="ignored Range"):
             await c.download_to_file("nasa", "partial.bin", dest)
 
-    # File must be unchanged — corruption avoided.
+    # The .part file must be unchanged and dest must not exist — corruption avoided.
-    assert dest.read_bytes() == b"X" * 100
+    assert part.read_bytes() == b"X" * 100
+    assert not dest.exists()
 
 
 async def test_resume_with_correct_206_succeeds(tmp_path):
     full_body = b"0123456789ABCDEF" * 16  # 256 bytes
     dest = tmp_path / "resume.bin"
-    dest.write_bytes(full_body[:64])  # we already have first 64 bytes
+    part = tmp_path / "resume.bin.part"
+    part.write_bytes(full_body[:64])  # we already have first 64 bytes in staging
 
     def handler(req: httpx.Request) -> httpx.Response:
         assert req.headers.get("Range") == "bytes=64-"
@@ -139,12 +142,15 @@ async def test_resume_with_correct_206_succeeds(tmp_path):
     assert result["bytes_written"] == len(full_body)
     assert result["resumed_from"] == 64
     assert result["md5_ok"] is True
+    # On success the .part is atomically renamed to dest.
     assert dest.read_bytes() == full_body
+    assert not part.exists()
 
 
 async def test_resume_with_wrong_content_range_start_raises(tmp_path):
     dest = tmp_path / "off.bin"
-    dest.write_bytes(b"X" * 100)
+    part = tmp_path / "off.bin.part"
+    part.write_bytes(b"X" * 100)
 
     def handler(req: httpx.Request) -> httpx.Response:
         # Server returns 206 but with WRONG starting offset
@@ -158,7 +164,9 @@ async def test_resume_with_wrong_content_range_start_raises(tmp_path):
         with pytest.raises(ArchiveError, match="Content-Range start"):
             await c.download_to_file("nasa", "off.bin", dest)
 
-    assert dest.read_bytes() == b"X" * 100  # unchanged
+    # .part unchanged, dest never created.
+    assert part.read_bytes() == b"X" * 100
+    assert not dest.exists()
 
 
 # ---------- H4: error body surfacing ----------
@@ -328,6 +336,7 @@ async def test_stream_abort_raises_archive_error_with_byte_count(tmp_path):
         return httpx.Response(200, content=evil_body())
 
     dest = tmp_path / "interrupted.bin"
+    part = tmp_path / "interrupted.bin.part"
     async with _client_with(handler) as c:
         with pytest.raises(ArchiveError) as exc_info:
             await c.download_to_file("nasa", "interrupted.bin", dest)
@@ -335,8 +344,9 @@ async def test_stream_abort_raises_archive_error_with_byte_count(tmp_path):
     msg = str(exc_info.value)
     assert "interrupted after" in msg
     assert "ReadError" in msg
-    # Partial bytes ARE on disk — at least the first delivered chunk.
+    # Partial bytes go to .part, NOT dest. dest stays absent until success.
-    on_disk = dest.read_bytes()
+    assert not dest.exists()
+    on_disk = part.read_bytes()
     assert len(on_disk) > 0
     assert on_disk == chunk_payload[: len(on_disk)]
 
@@ -360,4 +370,82 @@ async def test_fresh_download_writes_full_body(tmp_path):
     assert result["bytes_written"] == len(body)
     assert result["resumed_from"] == 0
     assert result["md5_ok"] is True
+    assert result["already_complete"] is False
+    # The atomic-rename pattern leaves no .part artifact after success.
     assert dest.read_bytes() == body
+    assert not (tmp_path / "new.bin.part").exists()
+
+
+# ---------- Atomic .part staging ----------
+
+
+async def test_failed_download_leaves_no_dest_file(tmp_path):
+    """A failed fresh download must NOT leave the final dest file as zero bytes —
+    it should leave only the .part staging file (or nothing if no bytes arrived)."""
+
+    def handler(req: httpx.Request) -> httpx.Response:
+        return httpx.Response(500, text="upstream cdn miss")
+
+    dest = tmp_path / "shouldfail.bin"
+    async with _client_with(handler) as c:
+        with pytest.raises(ArchiveError, match="HTTP 500"):
+            await c.download_to_file("nasa", "shouldfail.bin", dest)
+
+    # Critical: dest must NOT exist as an empty file misleading the user.
+    assert not dest.exists()
+
+
+async def test_already_complete_short_circuits_without_network(tmp_path):
+    """If dest exists and no .part, a follow-up download must not hit the
+    network — the file is already complete."""
+    dest = tmp_path / "done.bin"
+    dest.write_bytes(b"already-here")
+
+    calls = {"n": 0}
+
+    def handler(req: httpx.Request) -> httpx.Response:
+        calls["n"] += 1
+        return httpx.Response(500, text="should never fire")
+
+    async with _client_with(handler) as c:
+        result = await c.download_to_file("nasa", "done.bin", dest)
+
+    assert calls["n"] == 0  # no network at all
+    assert result["already_complete"] is True
+    assert result["bytes_written"] == len(b"already-here")
+    assert dest.read_bytes() == b"already-here"
+
+
+async def test_already_complete_verifies_md5_against_existing_file(tmp_path):
+    """If verify_md5 is passed and dest is complete, we re-hash to confirm."""
+    body = b"on-disk-content"
+    dest = tmp_path / "done.bin"
+    dest.write_bytes(body)
+
+    def handler(req: httpx.Request) -> httpx.Response:
+        return httpx.Response(500, text="should never fire")
+
+    async with _client_with(handler) as c:
+        result = await c.download_to_file(
+            "nasa", "done.bin", dest, verify_md5=hashlib.md5(body).hexdigest()
+        )
+
+    assert result["already_complete"] is True
+    assert result["md5_ok"] is True
+
+
+async def test_already_complete_md5_mismatch_caught(tmp_path):
+    """If the existing file's MD5 doesn't match expected, surface md5_ok=False."""
+    dest = tmp_path / "wrong.bin"
+    dest.write_bytes(b"actual-content")
+
+    def handler(req: httpx.Request) -> httpx.Response:
+        return httpx.Response(500, text="should never fire")
+
+    async with _client_with(handler) as c:
+        result = await c.download_to_file(
+            "nasa", "wrong.bin", dest, verify_md5="0" * 32
+        )
+    assert result["already_complete"] is True
+    assert result["md5_ok"] is False
+    assert result["md5_expected"] == "0" * 32

tests/test_server_mocked.py

@@ -10,6 +10,7 @@ These exercise the MCP tool functions directly and verify:
 from __future__ import annotations
 
 import asyncio
+import os
 from contextlib import asynccontextmanager
 
 import httpx
@@ -21,8 +22,10 @@ from mcarchive_org.server import (
     _enrich_doc,
     _normalize_collection,
     download_file,
+    get_download_root,
     get_item_metadata,
     search_items,
+    set_download_root,
 )
 
 
@@ -170,6 +173,75 @@ async def test_concurrent_downloads_same_file_are_serialized(tmp_path, monkeypat
     assert state["max_active"] == 1
 
 
+# ---------- runtime download root management ----------
+
+
+def test_get_download_root_reports_env_value(tmp_path, monkeypatch):
+    monkeypatch.setenv("MCARCHIVE_DOWNLOAD_ROOT", str(tmp_path))
+    info = get_download_root()
+    assert info["download_root"] == str(tmp_path.resolve())
+    assert info["source"] == "MCARCHIVE_DOWNLOAD_ROOT env var"
+    assert info["raw_env_value"] == str(tmp_path)
+
+
+def test_get_download_root_reports_default_when_no_env(monkeypatch):
+    monkeypatch.delenv("MCARCHIVE_DOWNLOAD_ROOT", raising=False)
+    info = get_download_root()
+    assert info["source"] == "default (./downloads under server CWD)"
+    assert info["raw_env_value"] is None
+
+
+def test_set_download_root_changes_env_and_creates_dir(tmp_path, monkeypatch):
+    monkeypatch.delenv("MCARCHIVE_DOWNLOAD_ROOT", raising=False)
+    target = tmp_path / "new" / "spot"
+    assert not target.exists()
+
+    info = set_download_root(path=str(target))
+
+    assert info["download_root"] == str(target.resolve())
+    assert info["changed"] is True
+    assert target.exists() and target.is_dir()
+    assert os.environ["MCARCHIVE_DOWNLOAD_ROOT"] == str(target.resolve())
+
+
+def test_set_download_root_expands_tilde(tmp_path, monkeypatch):
+    monkeypatch.delenv("MCARCHIVE_DOWNLOAD_ROOT", raising=False)
+    monkeypatch.setenv("HOME", str(tmp_path))
+
+    info = set_download_root(path="~/dl")
+
+    assert info["download_root"] == str((tmp_path / "dl").resolve())
+    assert (tmp_path / "dl").exists()
+
+
+@pytest.mark.parametrize("forbidden", ["/etc", "/usr/local", "/var/log", "/", "/sys"])
+def test_set_download_root_refuses_system_dirs(forbidden):
+    with pytest.raises(ValueError, match="system directory"):
+        set_download_root(path=forbidden)
+
+
+async def test_set_download_root_takes_effect_for_next_download(tmp_path, monkeypatch):
+    """The lazy-resolved root means a runtime change is honored by download_file
+    on the very next call without restarting."""
+    monkeypatch.delenv("MCARCHIVE_DOWNLOAD_ROOT", raising=False)
+    set_download_root(path=str(tmp_path / "first"))
+
+    def handler(req):
+        return httpx.Response(200, content=b"data")
+
+    async with swap_shared_client(handler):
+        await download_file(identifier="nasa", filename="a.bin", overwrite=True)
+        # Now move the root to a different directory mid-session.
+        set_download_root(path=str(tmp_path / "second"))
+        await download_file(identifier="nasa", filename="b.bin", overwrite=True)
+
+    assert (tmp_path / "first" / "nasa" / "a.bin").exists()
+    assert (tmp_path / "second" / "nasa" / "b.bin").exists()
+
+
+# ---------- M2 (continued): cross-file parallelism ----------
+
+
 async def test_concurrent_downloads_different_files_run_in_parallel(tmp_path, monkeypatch):
     """Different filenames get different locks — they should run concurrently."""
     monkeypatch.setenv("MCARCHIVE_DOWNLOAD_ROOT", str(tmp_path))