Fix JSON output: omit null values and add trailing newline

[amc-corey-cox]

Summary

• Fixes Slot suppression doesn't work with JSON output serialisation #139: JSON output now omits keys with None values, matching YAML serialization behavior. Slot suppression via expr: None if ... now works correctly for JSON output.
• Fixes Missing final newline character in JSON output #141: JSON and JSONL single-object output now ends with a trailing newline character.

Changes

• Added _strip_nulls() helper in output_streams.py that recursively removes None values from dicts before JSON serialization
• Applied to all JSON/JSONL code paths: dump_output(), JSONStreamWriter, JSONLStreamWriter, json_stream(), jsonl_stream()
• Added trailing \n to JSON/JSONL output in dump_output() (streaming paths already had this)

Test plan

• 5 new tests in test_output_streams.py — null suppression for all JSON/JSONL writers + nested nulls
• 3 new tests in test_cli.py — trailing newline and null suppression via dump_output()
• Full test suite passes (493 passed, 4 skipped)

🤖 Generated with Claude Code

[Copilot]

Pull request overview

This PR aligns JSON/JSONL output behavior with existing YAML behavior by omitting None-valued keys, and ensures JSON/JSONL CLI output ends with a trailing newline (fixing console prompt “run-on” and Unix text conventions).

Changes:

• Add _strip_nulls() helper to recursively remove None values from dictionaries prior to JSON/JSONL serialization.
• Apply null-stripping across all JSON/JSONL stream writer code paths (JSONStreamWriter, JSONLStreamWriter, json_stream, jsonl_stream) and CLI dump_output().
• Ensure dump_output() JSON and JSONL output always ends with \n, and add tests covering null suppression + newline behavior.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated no comments.

File	Description
src/linkml_map/writers/output_streams.py	Adds _strip_nulls() and applies it to all JSON/JSONL streaming serialization paths.
src/linkml_map/cli/cli.py	Updates dump_output() JSON/JSONL branches to strip nulls and append trailing newline.
tests/test_writers/test_output_streams.py	Adds unit tests asserting JSON/JSONL streaming omits None keys (including nested dicts).
tests/test_cli/test_cli.py	Adds CLI-level tests for trailing newline and null suppression in dump_output().

Comments suppressed due to low confidence (1)

tests/test_cli/test_cli.py:7

• The standard-library imports in this file are now out of order (adding import json before from collections.abc ... breaks Ruff/isort sorting). Please reorder the import block to match the project’s isort configuration so linting passes.

"""Tests all command-line subcommands."""

import json
from collections.abc import Generator
from pathlib import Path
import re
from typing import Any, Optional, Union