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Beside one public API change, the appearance and behavior of NEST should remain unchanged. The refactoring contains:\r\n\r\n* The classes `Network`, `Scheduler`, `Communicator` and `ConnectionManager` are marked deprecated and will be removed in the future.\r\n* Their functionality is moved into `Manager` classes:\r\n    * `ConnectionBuilderManager` (will be renamed to `ConnectionManager` later) is responsible for storing, creating and managing connections.\r\n    * `EventDeliveryManager` is responsible for delivering events, both local and remote.\r\n    * `IOManager` is responsible for file IO with the operating system.\r\n    * `LoggingManager` is responsible for creating and distributing logging events (former `Network::message(...)` method).\r\n    * `ModelManager` is responsible for storing node and synapse models and creating new instances from these models.\r\n    * `ModelRangeManager` stores the node model for ranges of nodes.\r\n    * `MPIManager` is responsible for all MPI communication.\r\n    * `MUSICManager` is responsible for all MUSIC related interactions.\r\n    * `NodeManager` is responsible for storing and managing all node objects.\r\n    * `RNGManager` is responsible for creation and access to all random number generators.\r\n    * `SimulationManager` is responsible for starting, stopping and resuming simulations.\r\n    * `SPManager` is responsible for structural plasticity.\r\n    * `VPManager` is responsible for threading and the management of virtual processes.\r\n* The `KernelManager` gives easy access to all `Manager` classes via the function `nest::kernel()`.\r\n* [API change] The `min_delay` and `max_delay` setting and checking is moved from the `ConnectorModel` to the `DelayChecker`s, which are managed by the `ConnectionBuilderManager`. Therefore, the `*_delay` is not set on the default synapse types any more, but during the `SetKernelStatus`.\r\n* Sort the header includes according to the guidelines. Also add the script `extras/include_checker.py` that suggests an include order for a file or the files in a directory.\r\n* Each module contain the beginning for a public NEST API, that can be used to program NEST on the C++ level. The corresponding `SLIModule`s are implemented on top of this API (ongoing work).\r\n\r\nI hope I did not miss any changes. I invite you all (@nest/nest-developers) to review and test this PR. @janhahne please see that the gap junctions work as expected. @sdiazpier and @naveau please see that the structural plasticity is working as expected. 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