fix: resolve all test failures and improve test infrastructure

- Fix visualization schema tests to use correct tool paths (tools/visualize_schema.py)
- Fix cache management test to use project cache directory consistently
- Add missing toml dependency for frontmatter support
- Create comprehensive DEPENDENCIES.md documentation
- Achieve 100% test pass rate (800/800 tests passing)

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

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

DEPENDENCIES.md

@@ -0,0 +1,92 @@
+# MarkiTect Project Dependencies
+
+## Overview
+This document lists all project dependencies for the MarkiTect project.
+
+## Production Dependencies
+These are required for running the application:
+
+- **markdown-it-py** - Markdown parsing library
+- **PyYAML** - YAML file processing
+- **click>=8.0.0** - Command-line interface framework
+- **tabulate>=0.9.0** - Table formatting for output
+- **jsonpath-ng>=1.5.0** - JSONPath query support
+- **aiohttp>=3.8.0** - Async HTTP client/server
+- **toml** - TOML file parsing (for frontmatter support)
+
+## Development Dependencies
+These are required for development, testing, and code quality:
+
+- **pytest** - Testing framework
+- **pytest-cov** - Test coverage reporting
+- **black** - Code formatting
+- **flake8** - Code linting
+- **mypy** - Type checking
+
+## Test Dependencies
+Additional dependencies for testing (from tests/requirements-test.txt if present):
+- See `tests/requirements-test.txt` for any additional test-specific dependencies
+
+## Installation
+
+### Quick Setup
+```bash
+# Install production dependencies only
+pip install -e .
+
+# Install with development dependencies
+make dev
+```
+
+### Manual Installation
+```bash
+# Production dependencies
+pip install markdown-it-py PyYAML click>=8.0.0 tabulate>=0.9.0 jsonpath-ng>=1.5.0 aiohttp>=3.8.0 toml
+
+# Development dependencies
+pip install pytest pytest-cov black flake8 mypy
+```
+
+### Virtual Environment Setup
+```bash
+# Create and activate virtual environment
+python3 -m venv .venv
+source .venv/bin/activate
+
+# Install dependencies
+make dev
+```
+
+## Running Tests
+After installing dependencies:
+
+```bash
+# Run all tests
+make test
+
+# Run tests with coverage
+pytest --cov
+
+# Run specific test layers
+make test-foundation
+make test-infrastructure
+make test-integration
+```
+
+## Code Quality Tools
+
+```bash
+# Format code
+make format
+
+# Run linting
+make lint
+
+# Type checking
+mypy markitect/
+```
+
+## Notes
+- Python 3.8+ is required
+- Virtual environment (.venv) is recommended
+- All dependencies are managed through pyproject.toml