fix: preserve incremental step order on clone

[fengjikui]

Summary

Refs #3838.

This preserves the explicit pipe position of an existing incremental step when a resource is cloned and its hints/config wrappers are ejected and injected again. The issue was that hint-based incremental replacement during clone removed the existing incremental transform and re-added it through the default affinity-based append path, which could move user-inserted steps such as MetricsItem before incremental filtering.

The fix records the current incremental step index before replacement/ejection and passes that index back into set_incremental when the incremental is reinserted. Normal first-time incremental insertion still uses the existing affinity behavior.

Validation

• uv run --with duckdb --with pyarrow --with pydantic pytest tests/extract/test_incremental.py::test_clone_preserves_inserted_step_after_hints_incremental tests/extract/test_incremental.py::test_pydantic_columns_validator tests/extract/test_extract.py::test_add_metrics tests/extract/test_extract.py::test_custom_metrics_preserved_when_all_items_filtered -q -> 6 passed in 1.37s
• uv run ruff check dlt/extract/resource.py tests/extract/test_incremental.py -> All checks passed!
• python3 -m py_compile dlt/extract/resource.py tests/extract/test_incremental.py -> passed

I also ran the issue-style pipeline.run reproduction locally after the fix and observed row_count: 2, so the metrics step now sees only rows that survive incremental filtering.