feat: reorganize tests by capability with separate test targets

Separate capability-specific tests from core system tests to establish clear
test organization and separation of concerns.

## Test Reorganization:
- **markitect-content tests**: Moved 6 tests to capabilities/markitect-content/tests/
- **markitect-finance tests**: Moved 7 tests to markitect/finance/tests/
- **markitect-query tests**: Moved 1 test to markitect/query_paradigms/tests/
- **markitect-graphql tests**: Moved 2 tests to markitect/graphql/tests/
- **markitect-plugins tests**: Moved 2 tests to markitect/plugins/tests/

## Makefile Updates:
- **make test**: Excludes capability tests, runs only core system tests
- **make test-capabilities**: Runs all capability tests
- **make test-capability-***: Individual capability test targets
- Updated all test targets (test-red, test-green, test-ultra-fast, test-perf)
- Added capability test targets to help documentation

## Benefits:
- Clear separation between core system tests and capability-specific tests
- Faster core test execution (capability tests not run by default)
- Individual capability testing for focused development
- Supports future capability extraction workflow
- Maintains capability test independence

Test verification:
- Core tests: 1291 tests (capability tests excluded)
- Finance capability: 143 tests working independently
- Content capability: 79 tests working independently

🤖 Generated with [Claude Code](https://claude.ai/code)

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

capabilities/markitect-content/tests/test_markdownmatters_integration.py

@@ -0,0 +1,295 @@
+"""
+Integration tests for complete MarkdownMatters CLI implementation.
+Tests all four command families working together.
+"""
+
+import pytest
+import tempfile
+import os
+from pathlib import Path
+from click.testing import CliRunner
+
+from markitect_content.commands import content_get, content_stats
+from markitect.matter_frontmatter.commands import frontmatter_get, frontmatter_keys
+from markitect.matter_contentmatter.commands import contentmatter_get, contentmatter_keys
+from markitect.matter_tailmatter.commands import tailmatter_get, tailmatter_check
+
+
+class TestMarkdownMattersIntegration:
+    """Test complete MarkdownMatters functionality integration."""
+
+    @pytest.fixture
+    def complete_document(self):
+        """A complete MarkdownMatters document with all three zones."""
+        return """---
+title: "Complete MarkdownMatters Document"
+author: "Integration Test"
+version: 1.0
+status: "testing"
+---
+
+# Complete MarkdownMatters Document
+
+This document demonstrates all three matter zones working together.
+
+Author: Dr. Test Researcher
+Institution: MarkdownMatters University
+Email: test@markdownmatters.edu
+Project: Integration Testing
+Version: 2.0
+Status: Active
+
+## Research Content
+
+Research Method: Integration Testing
+Sample Size: Complete document
+Test Framework: MarkdownMatters CLI
+
+The content includes various MultiMarkdown key-value pairs that provide contextual metadata.
+
+## Results
+
+Result Status: All systems operational
+Performance: Excellent
+Coverage: 100%
+
+All matter zones are properly separated and accessible through their respective CLI commands.
+
+---
+
+```yaml tailmatter
+qa_checklist:
+  - requirement: "All three matter zones tested"
+    complete: true
+  - requirement: "CLI commands validated"
+    complete: true
+  - requirement: "Integration verified"
+    complete: false
+
+editorial:
+  status: "Integration Testing"
+  reviewer: "integration.tester@markdownmatters.edu"
+  version: 3.0
+
+agent_config:
+  role: "integration_validator"
+  access_scope: "all_zones"
+  validation_mode: "comprehensive"
+```"""
+
+    @pytest.fixture
+    def runner(self):
+        """CLI test runner."""
+        return CliRunner()
+
+    def test_all_command_families_work_on_same_document(self, runner, complete_document):
+        """Test that all four command families can process the same document."""
+        with tempfile.NamedTemporaryFile(mode='w', suffix='.md', delete=False) as f:
+            f.write(complete_document)
+            temp_file = f.name
+
+        try:
+            # Test content commands
+            result = runner.invoke(content_get, ['--file', temp_file])
+            assert result.exit_code == 0
+            assert "Complete MarkdownMatters Document" in result.output
+            assert "---" not in result.output  # No frontmatter
+            assert "qa_checklist" not in result.output  # No tailmatter
+
+            result = runner.invoke(content_stats, ['--file', temp_file])
+            assert result.exit_code == 0
+            assert "word_count" in result.output
+
+            # Test frontmatter commands
+            result = runner.invoke(frontmatter_get, ['title', '--file', temp_file])
+            assert result.exit_code == 0
+            assert "Complete MarkdownMatters Document" in result.output
+
+            result = runner.invoke(frontmatter_keys, ['--file', temp_file])
+            assert result.exit_code == 0
+            assert "title" in result.output
+            assert "author" in result.output
+
+            # Test contentmatter commands
+            result = runner.invoke(contentmatter_get, ['Author', '--file', temp_file])
+            assert result.exit_code == 0
+            assert "Dr. Test Researcher" in result.output
+
+            result = runner.invoke(contentmatter_keys, ['--file', temp_file])
+            assert result.exit_code == 0
+            assert "Author" in result.output
+            assert "Institution" in result.output
+
+            # Test tailmatter commands
+            result = runner.invoke(tailmatter_get, ['editorial.status', '--file', temp_file])
+            assert result.exit_code == 0
+            assert "Integration Testing" in result.output
+
+            result = runner.invoke(tailmatter_check, ['--file', temp_file])
+            assert result.exit_code == 0
+            assert "QA Checklist Status" in result.output
+            assert "✅" in result.output
+            assert "❌" in result.output
+
+        finally:
+            os.unlink(temp_file)
+
+    def test_matter_zone_separation(self, runner, complete_document):
+        """Test that each command family only accesses its designated zone."""
+        with tempfile.NamedTemporaryFile(mode='w', suffix='.md', delete=False) as f:
+            f.write(complete_document)
+            temp_file = f.name
+
+        try:
+            # Frontmatter should not include contentmatter or tailmatter
+            result = runner.invoke(frontmatter_keys, ['--file', temp_file])
+            assert "Author" not in result.output  # This is contentmatter
+            assert "qa_checklist" not in result.output  # This is tailmatter
+
+            # Contentmatter should not include frontmatter or tailmatter
+            result = runner.invoke(contentmatter_keys, ['--file', temp_file])
+            assert "title" not in result.output  # This is frontmatter
+            assert "qa_checklist" not in result.output  # This is tailmatter
+
+            # Content should not include any matter zones in the actual content
+            result = runner.invoke(content_get, ['--file', temp_file])
+            assert "title:" not in result.output  # No frontmatter YAML
+            assert "qa_checklist:" not in result.output  # No tailmatter YAML
+
+        finally:
+            os.unlink(temp_file)
+
+    def test_performance_with_large_document(self, runner):
+        """Test performance with a large document containing all matter zones."""
+        # Create a large document
+        large_content = []
+        large_content.append("---")
+        large_content.append("title: 'Large Document Performance Test'")
+        for i in range(50):
+            large_content.append(f"field_{i}: 'value_{i}'")
+        large_content.append("---")
+        large_content.append("")
+
+        large_content.append("# Large Document Performance Test")
+        large_content.append("")
+
+        # Add many contentmatter pairs
+        for i in range(100):
+            large_content.append(f"Data Field {i}: Value for field {i}")
+            large_content.append("")
+
+        # Add substantial content
+        for i in range(50):
+            large_content.append(f"## Section {i}")
+            large_content.append("")
+            large_content.append(f"Content for section {i} with detailed information and multiple paragraphs.")
+            large_content.append("")
+            large_content.append("More content here to make the document substantial in size.")
+            large_content.append("")
+
+        large_content.append("---")
+        large_content.append("")
+        large_content.append("```yaml tailmatter")
+        large_content.append("qa_checklist:")
+        for i in range(20):
+            complete = "true" if i % 3 == 0 else "false"
+            large_content.append(f"  - requirement: 'Test requirement {i}'")
+            large_content.append(f"    complete: {complete}")
+        large_content.append("editorial:")
+        large_content.append("  status: 'Performance Testing'")
+        large_content.append("```")
+
+        large_document = "\n".join(large_content)
+
+        with tempfile.NamedTemporaryFile(mode='w', suffix='.md', delete=False) as f:
+            f.write(large_document)
+            temp_file = f.name
+
+        try:
+            # Test that all commands complete in reasonable time
+            import time
+
+            start_time = time.time()
+            result = runner.invoke(content_stats, ['--file', temp_file])
+            content_time = time.time() - start_time
+            assert result.exit_code == 0
+            assert content_time < 2.0  # Should complete in under 2 seconds
+
+            start_time = time.time()
+            result = runner.invoke(frontmatter_keys, ['--file', temp_file])
+            frontmatter_time = time.time() - start_time
+            assert result.exit_code == 0
+            assert frontmatter_time < 1.0  # Should complete in under 1 second
+
+            start_time = time.time()
+            result = runner.invoke(contentmatter_keys, ['--file', temp_file])
+            contentmatter_time = time.time() - start_time
+            assert result.exit_code == 0
+            assert contentmatter_time < 2.0  # Should complete in under 2 seconds
+
+            start_time = time.time()
+            result = runner.invoke(tailmatter_check, ['--file', temp_file])
+            tailmatter_time = time.time() - start_time
+            assert result.exit_code == 0
+            assert tailmatter_time < 1.0  # Should complete in under 1 second
+
+        finally:
+            os.unlink(temp_file)
+
+    def test_error_handling_consistency(self, runner):
+        """Test that all command families handle errors consistently."""
+        non_existent_file = "/tmp/non_existent_file.md"
+
+        # All commands should handle missing files gracefully
+        commands_and_args = [
+            (content_get, ['--file', non_existent_file]),
+            (content_stats, ['--file', non_existent_file]),
+            (frontmatter_get, ['title', '--file', non_existent_file]),
+            (frontmatter_keys, ['--file', non_existent_file]),
+            (contentmatter_get, ['Author', '--file', non_existent_file]),
+            (contentmatter_keys, ['--file', non_existent_file]),
+            (tailmatter_get, ['editorial.status', '--file', non_existent_file]),
+            (tailmatter_check, ['--file', non_existent_file]),
+        ]
+
+        for command, args in commands_and_args:
+            result = runner.invoke(command, args)
+            assert result.exit_code != 0  # Should fail for non-existent file
+
+    def test_help_commands_consistency(self, runner):
+        """Test that all commands provide consistent help."""
+        commands = [
+            content_get, content_stats,
+            frontmatter_get, frontmatter_keys,
+            contentmatter_get, contentmatter_keys,
+            tailmatter_get, tailmatter_check
+        ]
+
+        for command in commands:
+            result = runner.invoke(command, ['--help'])
+            assert result.exit_code == 0
+            assert "Usage:" in result.output
+            assert "--help" in result.output
+
+    def test_output_format_consistency(self, runner, complete_document):
+        """Test that commands with format options work consistently."""
+        with tempfile.NamedTemporaryFile(mode='w', suffix='.md', delete=False) as f:
+            f.write(complete_document)
+            temp_file = f.name
+
+        try:
+            # Test JSON format consistency
+            result = runner.invoke(content_stats, ['--file', temp_file, '--format', 'json'])
+            assert result.exit_code == 0
+            assert result.output.startswith('{')
+
+            result = runner.invoke(frontmatter_keys, ['--file', temp_file, '--format', 'json'])
+            assert result.exit_code == 0
+            assert result.output.startswith('[')
+
+            result = runner.invoke(contentmatter_keys, ['--file', temp_file, '--format', 'json'])
+            assert result.exit_code == 0
+            assert result.output.startswith('[')
+
+        finally:
+            os.unlink(temp_file)