fix: log unreadable subtrees during size pre-flight

os.walk silently swallowed directory-listing errors, so a permission-denied
subtree could make a large repo under-count and slip past the pre-flight.
Surface such omissions via an onerror warning.

strix/interface/utils.py

@@ -1,5 +1,6 @@
 import ipaddress
 import json
+import logging
 import os
 import re
 import secrets
@@ -23,6 +24,9 @@ from rich.text import Text
 from strix.config import load_settings
 
 
+logger = logging.getLogger(__name__)
+
+
 def get_severity_color(severity: str) -> str:
     severity_colors = {
         "critical": "#dc2626",
@@ -1219,9 +1223,17 @@ def directory_size_bytes(path: Path) -> int:
     Best-effort: files that disappear or can't be stat'd mid-walk are skipped.
     Used as a cheap (stat-only) pre-flight to estimate the cost of streaming a
     local target into the sandbox before we actually try to copy it.
+
+    Directories that can't be listed (e.g. permission denied) are logged and
+    skipped rather than silently dropped — so an under-count is at least
+    visible — but the returned total then excludes their contents.
     """
+
+    def _on_walk_error(error: OSError) -> None:
+        logger.warning("Could not read %s while measuring size: %s", error.filename, error)
+
     total = 0
-    for root, _dirs, files in os.walk(path, followlinks=False):
+    for root, _dirs, files in os.walk(path, followlinks=False, onerror=_on_walk_error):
         for name in files:
             file_path = os.path.join(root, name)  # noqa: PTH118
             try:

tests/test_local_sources.py

@@ -2,6 +2,9 @@
 
 from __future__ import annotations
 
+import logging
+import os
+import sys
 from typing import TYPE_CHECKING, Any
 
 import pytest
@@ -49,6 +52,28 @@ def test_directory_size_skips_symlinks(tmp_path: Path) -> None:
     assert directory_size_bytes(tmp_path) == 100
 
 
+@pytest.mark.skipif(sys.platform == "win32", reason="relies on POSIX permissions")
+def test_directory_size_logs_and_skips_unreadable_subdir(
+    tmp_path: Path, caplog: pytest.LogCaptureFixture
+) -> None:
+    if hasattr(os, "geteuid") and os.geteuid() == 0:
+        pytest.skip("root bypasses directory permissions")
+    _write_file(tmp_path / "top.txt", 100)
+    locked = tmp_path / "locked"
+    locked.mkdir()
+    _write_file(locked / "secret.bin", 9999)
+    locked.chmod(0o000)
+    try:
+        with caplog.at_level(logging.WARNING):
+            size = directory_size_bytes(tmp_path)
+    finally:
+        locked.chmod(0o755)
+    # The unreadable subtree is excluded (not silently treated as readable) and
+    # the omission is logged rather than vanishing without a trace.
+    assert size == 100
+    assert any("Could not read" in record.message for record in caplog.records)
+
+
 def test_find_oversized_returns_nothing_under_limit(tmp_path: Path) -> None:
     _write_file(tmp_path / "a.txt", 100)
     targets = [_local_target(str(tmp_path))]