feat: Add project directory structure guidelines for maintainability and scalability

.github/instructions/copilot.instructions.md

@@ -85,3 +85,32 @@ applyTo: '**'
 
 **Summary:**
 This project is a modular, extensible Tkinter application for tracking medication and pathology data. Code should be clean, dynamic, user-friendly, and robust, following PEP8 and the architectural patterns already established. All new features or changes should integrate seamlessly with the existing managers and UI paradigms, unless instructed otherwise.
+
+
+**Notes:**
+A robust Python project directory structure is crucial for maintainability, scalability, and collaboration. Key best practices include:
+
+    Root Project Directory:
+        Create a top-level directory for your project, typically named after the project itself.
+    Source Code (src/ or my_package/):
+        Modern approach: Place all application source code within a src/ directory. This clearly separates source code from other project files.
+        Alternative: If your project is a single package, the main package directory (e.g., my_package/) can reside directly under the root, containing your modules and __init__.py.
+        Modularity: Break down your code into smaller, logical modules within this directory, each with a clear responsibility.
+        __init__.py: Include an __init__.py file in every directory intended to be a Python package, marking it as importable.
+    Tests (tests/):
+        Create a dedicated tests/ directory at the root level to house all your test files.
+        Structure tests to mirror the application's module structure for easier navigation and understanding.
+    Documentation (docs/):
+        Include a docs/ directory for project documentation, including usage guides, API references, and design documents.
+    Configuration (config/ or pyproject.toml):
+        Use pyproject.toml for modern project configuration, including project metadata, dependencies, and tool configurations (linters, formatters, test runners).
+        For application-specific or environment-dependent configurations, consider a config/ directory or environment variables.
+    Entry Point (main.py or cli.py):
+        Designate a clear entry point for your application, often main.py or cli.py for command-line interfaces. This file should primarily orchestrate the application's flow and delegate logic to other modules.
+    Other Important Files:
+        README.md: A comprehensive README at the root level providing project overview, installation instructions, and usage examples.
+        LICENSE: A license file specifying the terms of use and distribution.
+        .gitignore: For version control, specifying files and directories to be ignored by Git (e.g., virtual environments, compiled files, sensitive data).
+        requirements.txt: (or managed via pyproject.toml): Lists project dependencies.
+    Virtual Environments:
+        Utilize virtual environments (e.g., venv, conda) to isolate project dependencies and avoid conflicts. The virtual environment directory (e.g., .venv/) should be ignored by version control.