Add PowerShell scripts for server setup and integration testing

- Implemented `run-server.ps1` for setting up the Zen MCP server environment, including virtual environment creation, dependency installation, and Docker cleanup.
- Added logging and error handling throughout the setup process.
- Included functions for validating API keys and configuring integration with Claude Desktop and Gemini CLI.
- Created `run_integration_tests.ps1` to execute integration tests with real API calls, including checks for API key availability and environment setup.
- Enhanced output with color-coded messages for better user experience.

Patch directory added for cross-platform patching support (`patch_crossplatform.py`).

patch/README.md

@@ -0,0 +1,93 @@
+# Cross-Platform Compatibility Patches
+
+This directory contains patch scripts to improve the cross-platform compatibility of the zen-mcp server.
+
+## Files
+
+### `patch_crossplatform.py`
+Main script that automatically applies all necessary fixes to resolve cross-platform compatibility issues.
+
+**Usage:**
+```bash
+# From the patch/ directory
+python patch_crossplatform.py [--dry-run] [--backup] [--validate-only]
+```
+
+**Options:**
+- `--dry-run`: Show changes without applying them
+- `--backup`: Create a backup before modifying files
+- `--validate-only`: Only check if the fixes are already applied
+
+### `validation_crossplatform.py`
+Validation script that tests whether all fixes work correctly.
+
+**Usage:**
+```bash
+# From the patch/ directory
+python validation_crossplatform.py
+```
+
+## Applied Fixes
+
+1. **HOME DIRECTORY DETECTION ON WINDOWS:**
+   - Linux tests (/home/ubuntu) failed on Windows
+   - Unix patterns were not detected due to backslashes
+   - Solution: Added Windows patterns + double path check
+
+2. **UNIX PATH VALIDATION ON WINDOWS:**
+   - Unix paths (/etc/passwd) were rejected as relative paths
+   - Solution: Accept Unix paths as absolute on Windows
+
+3. **CROSS-PLATFORM TESTS:**
+   - Assertions used OS-specific separators
+   - The safe_files test used a non-existent file on Windows
+   - Solution: Use Path.parts + temporary files on Windows
+
+4. **SHELL SCRIPT COMPATIBILITY ON WINDOWS:**
+   - Shell scripts did not detect Windows virtual environment paths
+   - Solution: Added detection for .zen_venv/Scripts/ paths
+
+5. **COMMUNICATION SIMULATOR LOGGER BUG:**
+   - AttributeError: logger used before initialization
+   - Solution: Initialize logger before calling _get_python_path()
+
+6. **PYTHON PATH DETECTION ON WINDOWS:**
+   - The simulator could not find the Windows Python executable
+   - Solution: Added Windows-specific detection
+
+## How to Use
+
+1. **Apply all fixes:**
+   ```bash
+   cd patch/
+   python patch_crossplatform.py
+   ```
+
+2. **Test in dry-run mode (preview):**
+   ```bash
+   cd patch/
+   python patch_crossplatform.py --dry-run
+   ```
+
+3. **Validate the fixes:**
+   ```bash
+   cd patch/
+   python validation_crossplatform.py
+   ```
+
+4. **Check if fixes are already applied:**
+   ```bash
+   cd patch/
+   python patch_crossplatform.py --validate-only
+   ```
+
+## Modified Files
+
+- `utils/file_utils.py`: Home patterns + Unix path validation
+- `tests/test_file_protection.py`: Cross-platform assertions
+- `tests/test_utils.py`: Safe_files test with temporary file
+- `run_integration_tests.sh`: Windows venv detection
+- `code_quality_checks.sh`: venv and Windows tools detection
+- `communication_simulator_test.py`: Logger initialization order + Windows paths
+
+Tests should now pass on Windows, macOS, and Linux!