docs: add comprehensive documentation structure and API reference

Created topic-based documentation:
- basics.rst: core concepts and fundamental usage
- cyclic_programming.rst: PLC-style programming with Cycletools
- event_programming.rst: event-driven patterns and callbacks
- advanced.rst: gateway IOs, replace_io_file, watchdog management
- installation.rst and quickstart.rst: getting started guides

Added complete API reference in docs/api/:
- All device classes including ModularBaseConnect_4_5 and GatewayMixin
- I/O, helper, and main class documentation

Enhanced Sphinx configuration with RTD theme and improved autodoc settings.
Removed auto-generated modules.rst and revpimodio2.rst.

docs/api/revpimodio.rst

@@ -0,0 +1,141 @@
+==================
+RevPiModIO Classes
+==================
+
+Main classes for managing Revolution Pi hardware.
+
+.. currentmodule:: revpimodio2.modio
+
+RevPiModIO
+==========
+
+.. autoclass:: RevPiModIO
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :special-members: __init__
+
+   Main class for managing all devices and IOs from the piCtory configuration.
+
+   This class manages the complete piCtory configuration and loads all devices
+   and IOs. It handles exclusive management of the process image and ensures
+   data synchronization.
+
+   **Constructor Parameters:**
+
+   :param autorefresh: Automatically sync process image (recommended: True)
+   :type autorefresh: bool
+   :param monitoring: Read-only mode for supervision (no writes)
+   :type monitoring: bool
+   :param syncoutputs: Load current output values on initialization
+   :type syncoutputs: bool
+   :param debug: Enable detailed error messages and logging
+   :type debug: bool
+
+   **Key Attributes:**
+
+
+
+      Access to all configured inputs/outputs
+
+
+
+      Access to RevPi Core values (LEDs, status)
+
+
+
+      Access to specific devices by name
+
+
+
+      Update frequency in milliseconds
+
+
+
+      Threading event for clean shutdown
+
+
+
+      Count of read/write failures
+
+
+
+      Exception threshold (0 = disabled)
+
+   **Example:**
+
+   .. code-block:: python
+
+       import revpimodio2
+
+       # Initialize with auto-refresh
+       rpi = revpimodio2.RevPiModIO(autorefresh=True)
+
+       # Access IOs
+       if rpi.io.button.value:
+           rpi.io.led.value = True
+
+       # Clean shutdown
+       rpi.exit()
+
+Loop Execution Methods
+----------------------
+
+
+Data Synchronization Methods
+-----------------------------
+
+
+Utility Methods
+---------------
+
+
+RevPiModIOSelected
+==================
+
+.. autoclass:: RevPiModIOSelected
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :special-members: __init__
+
+   Manage only specific devices from the piCtory configuration.
+
+   Use this class when you only need to control specific devices instead of
+   loading the entire configuration.
+
+   **Example:**
+
+   .. code-block:: python
+
+       # Manage only specific devices
+       rpi = revpimodio2.RevPiModIOSelected("DIO_Module_1", "AIO_Module_1")
+
+RevPiModIODriver
+================
+
+.. autoclass:: RevPiModIODriver
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :special-members: __init__
+
+   Write data to virtual device inputs for driver development.
+
+   **Example:**
+
+   .. code-block:: python
+
+       # Create driver for virtual device
+       driver = revpimodio2.RevPiModIODriver("VirtualDevice")
+
+DevSelect
+=========
+
+.. autoclass:: DevSelect
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :special-members: __init__
+
+   Customized search filter for RevPiModIOSelected.