The output location should both be a directory and not be directory

```console
> mkdir out
> codeql query run -d java-database -o out overrides.ql
A fatal error occurred: [redacted]/out is a directory.
> rmdir out
> codeql query run -d java-database -o out overrides.ql
A fatal error occurred: The output location [redacted]/out is not a directory, so only a single query can be executed.
```

`overrides.ql` is taken from https://help.semmle.com/QL/learn-ql/java/annotations.html

```codeql
import java

from Method overriding, Method overridden
where overriding.overrides(overridden) and
not overriding.getAnAnnotation() instanceof OverrideAnnotation
select overriding, "Method overrides another method, but does not have an @Override annotation."
```

```console
> codeql version
CodeQL command-line toolchain.
Version: 2.2.3.
Copyright (C) 2019-2020 GitHub, Inc.
Unpacked in: /nix/store/s5zfg5vzrfrfc3mqyh3g0r4r6mpqc2g1-codeql-2.2.3/codeql
Analysis results depend critically on separately distributed query and
extractor modules. To list modules that are visible to the toolchain,
use 'codeql resolve qlpacks' and 'codeql resolve languages'.
> uname -a
Linux nixos 5.9.1 #1-NixOS SMP Sat Oct 17 06:31:22 UTC 2020 x86_64 GNU/Linux
> nixos-version
20.09.1500.edb26126d98 (Nightingale)
```

`-o out` を使って 2 つの `codeql query run` コマンドを再現し、`out` をまずディレクトリにしてから存在しない状態にして、異なるエラーを比較します。出力先の CLI 処理を追跡し、単一のクエリと複数のクエリで意図されている動作を特定します。両方のケースで出力先の動作に一貫性があり、カバーされていれば完了です。

索引モデルが issue の本文から書いたものです。