Migrate from PyYAML to ruamel.yaml

Replace PyYAML with ruamel.yaml for round-trip-safe YAML serialization. Critical for git-native storage where programmatic edits should not reformat entire files.

Problem

PyYAML's `safe_dump` does not preserve comments, blank lines, quoting style, or flow/block style choices. When Pyrite programmatically updates an entry (adds a tag, changes a date), the entire frontmatter gets reformatted, producing noisy git diffs that obscure the actual change.

Scope

Add `ruamel.yaml` to dependencies

Create `pyrite/utils/yaml.py` with `load_yaml()`, `dump_yaml()`, `load_yaml_file()`, `dump_yaml_file()` wrappers

Migrate ~12 call sites from `yaml.safe_load`/`yaml.safe_dump` to wrapper functions

Update `Entry.to_markdown()` and `Entry.from_markdown()`

Add round-trip fidelity tests (load → save → diff shows no changes)

Evaluate removing PyYAML dependency

Key Files

`pyproject.toml` — dependency change

`pyrite/utils/yaml.py` — new wrapper module

`pyrite/models/base.py` — to_markdown, from_markdown

`pyrite/schema.py` — KBSchema.from_yaml

`pyrite/config.py` — config load/save

`pyrite/storage/repository.py` — frontmatter parsing

`pyrite/services/repo_service.py` — kb.yaml loading

`pyrite/github_auth.py` — auth config

Acceptance Criteria

[ ] All existing tests pass with ruamel.yaml

[ ] Round-trip test: load entry → save without changes → file is byte-identical

[ ] Round-trip test: load entry → change one field → save → diff shows only that field

[ ] Comments in kb.yaml preserved through load/save cycle

[ ] No formatting noise in git diffs from programmatic updates

Completed

Implemented in commit `46ea1d6`. Created `pyrite/utils/yaml.py` with round-trip wrappers using `ruamel.yaml.YAML()` with `preserve_quotes=True`. Migrated all call sites in config.py, base.py, schema.py, repository.py, repo_service.py, github_auth.py. 18 new tests in `tests/test_yaml_utils.py`. All 376 backend tests pass.

References

ADR-0008

Design Doc

Migrate from PyYAML to ruamel.yamlbacklog_item