[native_assets_cli] Cleanup JSON: version, out_dir, and out_file

[dcharkes]

Bug:

• [native_assets_cli] Remove fallback JSON encodings #2199

Cleanup of:

• Remove version from [native_assets_cli][native_assets_builder] Supporting version skew between SDK and build.dart #93
• Remove out_dir from [native_assets_cli] Deprecate and remove outputDirectory #2058
• Make out_file mandatory now it no longer has a fallback on out_dir.

[github-actions]

PR Health

Breaking changes ✔️

Package	Change	Current Version	New Version	Needed Version	Looking good?
native_assets_builder	Breaking	0.16.0	0.17.0-wip	0.17.0	✔️
native_assets_cli	Breaking	0.16.0	0.17.0-wip	0.17.0	✔️
native_toolchain_c	Non-Breaking	0.13.0	0.14.0-wip	0.13.1	✔️

API leaks ✔️

The following packages contain symbols visible in the public API, but not exported by the library. Export these symbols or remove them from your publicly visible API.

Package	Leaked API symbols

License Headers ✔️

// Copyright (c) 2025, the Dart project authors. Please see the AUTHORS file
// for details. All rights reserved. Use of this source code is governed by a
// BSD-style license that can be found in the LICENSE file.

Files
no missing headers

All source files should start with a license header.

Unrelated files missing license headers

Files
pkgs/jni/lib/src/third_party/generated_bindings.dart
pkgs/objective_c/lib/src/ns_input_stream.dart

[coveralls]

coverage: 77.554%. first build
when pulling d73bc76 on json-cleanup-outdir
into 75d4813 on main.

[goderbauer]

LGTM