Optimizations for the MRI persistence layer:

- Extract duplicated parse_mri/1 to shared macula_mri_khepri_parse module
- Add pagination support to list functions (list_children_opts, list_descendants_opts, list_by_type_opts) with limit/offset options
- Add depth limit to traverse_transitive via traverse_transitive_opts with max_depth option (default: 100)
- Implement config-driven indexing using enable_type_index and enable_realm_index app config
- Add warning log when type index is missing and fallback to tree scan occurs
- Simplify ensure_index_structure to no-op (Khepri auto-creates paths)
- Add 6 new tests for pagination and depth limit features

All 88 tests passing.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>