Fix tarball permission stripping and allowedTools flag format

[ElleNajt]

Summary

• Simplify _tar_inputs() to use tarfile.add() directly (preserves permissions by default)
• Fix --allowedTools CLI flag quoting using shlex.quote()
• Remove unnecessary mtime/uid/gid normalization (in-memory cache is sufficient)

Problem

The tarball creation was hardcoding all files to 0o644, stripping executable permissions. This caused Claude Code to see spurious 100755 -> 100644 permission changes when running git diff HEAD~1 --raw, leading to false positives.

Fix

Simplified from complex manual TarInfo construction to just:

def _tar_inputs(self, inputs: dict[str, Path], tar_path: Path) -> None:
    """Create a gzipped tarball from inputs, preserving file permissions."""
    with tarfile.open(tar_path, "w:gz") as tar:
        for name, local_path in sorted(inputs.items()):
            local_path = Path(local_path).expanduser().resolve()
            if not local_path.exists():
                raise CloudRunClientError(f"Input not found: {local_path}")
            tar.add(local_path, arcname=name)

This preserves file permissions naturally. The in-memory cache (keyed by path names) already prevents duplicate uploads within a process, so we dont need deterministic tarball hashes for GCS deduplication.

Test plan

• Permission preservation test passes (5 different modes: 0o755, 0o700, 0o750, 0o644, 0o444)
• In-memory caching tests pass
• Thread safety tests pass
• Removed obsolete deterministic tarring tests (no longer needed)

🤖 Generated with Claude Code