fix: prevent nested dict flattening in _create_at

[nathanjmcdougall]

Summary

Fixes a bug where Op.merge_into flattens nested dicts to the wrong indentation level when creating intermediate keys via _create_at.

Problem

When calling upsert("parent", "child", value={"x": 1, "y": 2}) on a document where parent doesn't exist, _create_at builds nested_value = {"child": {"x": 1, "y": 2}} and passes it to Op.merge_into("parent", nested_value). The Rust merge_into operation flattens the nested dict, producing:

parent:
  child:
  x: 1
  y: 2

instead of the correct:

parent:
  child:
    x: 1
    y: 2

Fix

Replace the single Op.merge_into call with a two-step approach:

1. Op.add(first_key, None) — creates the key with a placeholder
2. Op.replace(nested_value) on the new path — replaces with the full nested structure

Op.replace correctly serializes complex values, avoiding the flattening.

Testing

Adds a regression test (test_upsert_missing_nested_path_with_dict) that fails without the fix and passes with it. All 351 existing tests continue to pass.

[Copilot]

Pull request overview

Fixes incorrect YAML structure produced by Document.upsert() when creating missing intermediate keys whose value is a nested mapping, avoiding yamlpatch MergeInto’s uniform-indent serialization limitations.

Changes:

• Update _create_at() to route nested dict/list values through a two-step add placeholder + replace operation instead of merge_into.
• Add a regression test covering nested dict insertion via intermediate keys.
• Document merge_into’s flat-only constraint in Rust bindings and update the design spec accordingly.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 1 comment.

File	Description
tests/test_document.py	Adds regression test ensuring nested dict values remain properly nested when upserting through missing intermediate keys.
src/yamltrip/document.py	Implements conditional fallback to add + replace to preserve indentation for nested values when creating intermediate keys.
src/ops.rs	Documents merge_into as intended for flat/scalar-only updates and advises add + replace for nested values.
doc/specs/2026-05-13-yamltrip-design.md	Updates design notes to reflect the flat-vs-nested split in upsert() creation strategy.

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[Copilot]

Pull request overview

Copilot reviewed 4 out of 4 changed files in this pull request and generated 2 comments.

[Copilot]

Pull request overview

Copilot reviewed 4 out of 4 changed files in this pull request and generated 2 comments.

[Copilot]

Pull request overview

Copilot reviewed 5 out of 5 changed files in this pull request and generated 2 comments.

[Copilot]

Pull request overview

Copilot reviewed 5 out of 5 changed files in this pull request and generated 1 comment.

[Copilot]

Pull request overview

Copilot reviewed 5 out of 5 changed files in this pull request and generated 1 comment.

[Copilot]

Pull request overview

Copilot reviewed 6 out of 7 changed files in this pull request and generated 1 comment.