Add XML tree, semantic tree

[mattbriggs]

Summary by CodeRabbit

• New Features

  • Added reconciliation support for generic XML, JSON, and YAML documents.
  • Added built-in profiles with format-specific ordering behavior.
  • Added secure parsing limits and clear input validation errors.
  • Added unresolved-region reporting and configurable ambiguity handling.
  • CLI installation and missing-dependency guidance are now clearer.

• Bug Fixes

  • Ambiguous matches no longer produce misleading insert, delete, or localization presence findings.
  • Genuine, unambiguous differences remain reported accurately.

• Documentation

  • Expanded setup, CLI, API, profile, alignment, and classification guidance with JSON/YAML examples.

[coderabbitai]

Caution

Review failed

The pull request is closed.

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro Plus

Run ID: 153feee9-4f23-49e2-a69a-da43d44ddb02

📥 Commits

Reviewing files that changed from the base of the PR and between ad029db and 829f3e2.

📒 Files selected for processing (51)

• README.md
• _design/2026-08-11-Implementation-Note1.md
• _design/implementation-note-structural-reconciliation-iteration.md
• docs/api/cli.md
• docs/api/http.md
• docs/design/alignment.md
• docs/design/classification.md
• docs/development/extension-points.md
• docs/getting-started.md
• docs/profiles/authoring.md
• pyproject.toml
• src/reconciliation/adapters/data_tree/__init__.py
• src/reconciliation/adapters/data_tree/canonical_adapter.py
• src/reconciliation/adapters/data_tree/errors.py
• src/reconciliation/adapters/json/__init__.py
• src/reconciliation/adapters/json/canonical_adapter.py
• src/reconciliation/adapters/json/errors.py
• src/reconciliation/adapters/json/parser.py
• src/reconciliation/adapters/xml/canonical_adapter.py
• src/reconciliation/adapters/yaml/__init__.py
• src/reconciliation/adapters/yaml/canonical_adapter.py
• src/reconciliation/adapters/yaml/errors.py
• src/reconciliation/adapters/yaml/parser.py
• src/reconciliation/application/contracts/localization.py
• src/reconciliation/application/services/localization_validation.py
• src/reconciliation/core/alignment/aligner.py
• src/reconciliation/core/classification/classifiers/insert_delete.py
• src/reconciliation/core/classification/registry.py
• src/reconciliation/core/contracts/alignment.py
• src/reconciliation/core/contracts/profiles.py
• src/reconciliation/core/engine.py
• src/reconciliation/delivery/cli/app.py
• src/reconciliation/delivery/cli/entry.py
• src/reconciliation/delivery/composition.py
• src/reconciliation/profiles/generic_json_v1.yaml
• src/reconciliation/profiles/generic_xml_v1.yaml
• src/reconciliation/profiles/generic_yaml_v1.yaml
• src/reconciliation/reporting/html/templates/report.html.j2
• src/reconciliation/reporting/html/view_model.py
• src/reconciliation/reporting/summary_renderer.py
• tests/acceptance/test_ac_unresolved_alignment.py
• tests/integration/test_generic_json_pipeline.py
• tests/integration/test_generic_yaml_pipeline.py
• tests/unit/adapters/test_data_tree_adapter.py
• tests/unit/adapters/test_json_adapter.py
• tests/unit/adapters/test_profiles.py
• tests/unit/adapters/test_yaml_adapter.py
• tests/unit/application/test_ambiguity_guard.py
• tests/unit/core/test_unresolved_alignment.py
• tests/unit/delivery/test_cli.py
• tests/unit/delivery/test_orchestration.py

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📝 Walkthrough

Walkthrough

The change adds secure generic XML, JSON, and YAML adapters, canonical data-tree mappings, generic profiles, ambiguity-aware alignment and classification, CLI packaging updates, reporting fields, documentation, and broad test coverage.

Changes

Generic reconciliation and unresolved alignment

Layer / File(s)	Summary
Contracts, design, and documentation _design/..., docs/..., README.md	Documents generic adapters, canonical mappings, unresolved alignment states, presence policies, profiles, installation, and usage.
Secure parsing and canonical tree adapters src/reconciliation/adapters/...	Adds bounded JSON and YAML parsing, generic XML document adaptation, canonical data-tree construction, and structured errors.
Unresolved alignment and presence classification src/reconciliation/core/..., src/reconciliation/application/...	Adds unresolved alignment edges and regions, ambiguity-aware presence policies, diagnostics, localization filtering, and unresolved-region summaries.
Profiles, registry, delivery, and reporting src/reconciliation/profiles/..., src/reconciliation/delivery/..., src/reconciliation/reporting/..., pyproject.toml	Registers generic profiles, updates optional extras and the CLI entry point, and reports unresolved-region counts.
Adapter, pipeline, ambiguity, and delivery validation tests/...	Adds unit, integration, acceptance, profile, registry, and CLI coverage for the new behavior.

Estimated code review effort: 5 (Critical) | ~120 minutes

✨ Finishing Touches 💡 1

🛠️ Fix failing CI checks 💡

• Create stacked PR
• Commit on current branch

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch mdb_20260811_update

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