spams_sandbox: Ensured all types are from ctypes.
batch_learner: For the function batch_generate_save_neurons, quit passing and receiving using the expansion operators (* and **). Fixes issue #43.
advanced_image_processing: Cleaned up long lines. This is related to issue #41.
batch_learner: Cleaned up long lines. This is related to issue #41.
HDF5_logger: Cleaned up long lines. This is related to issue #41.
advanced_debugging: Cleaned up long lines. This is related to issue #41.
advanced_numpy: Cleaned up long lines. This is related to issue #41.
advanced_iterators: Cleaned up long lines. This is related to issue #41.
denoising: Cleaned up long lines. This is related to issue #41.
HDF5_searchers: Cleaned up long lines. This is related to issue #41.
simple_image_processing: Cleaned up long lines. This is related to issue #41.
tiff_file_format: Cleaned up long lines. This is related to issue #41.
advanced_numpy: Renamed to expanded_numpy.
expanded_numpy: Renamed from advanced_numpy.
__init__: Renamed advanced_numpy to expanded_numpy.
advanced_image_processing: Renamed advanced_numpy to expanded_numpy.
neuron_volumina_viewer: Renamed advanced_numpy to expanded_numpy.
tiff_file_format: Renamed advanced_numpy to expanded_numpy.

This is related to issue #40.
advanced_io: Renamed to additional_io.
additional_io: Renamed from advanced_io.
tiff_file_format: Renamed advanced_io to additional_io.

This is related to issue #40.
advanced_iterators: Renamed to additional_generators.
additional_generators: Renamed from advanced_iterators.
__init__: Renamed advanced_iterators to additional_generators.
advanced_image_processing: Renamed advanced_iterators to additional_generators.
expanded_numpy: Renamed advanced_iterators to additional_generators.
neuron_volumina_viewer: Renamed advanced_iterators to additional_generators.
tiff_file_format: Renamed advanced_iterators to additional_generators.

This is related to issue #40.
advanced_debugging: Renamed to debugging_tools.
debugging_tools: Renamed from advanced_debugging.
__init__: Renamed advanced_debugging to debugging_tools.
additional_generators: Renamed advanced_debugging to debugging_tools.
additional_io: Renamed advanced_debugging to debugging_tools.
advanced_image_processing: Renamed advanced_debugging to debugging_tools.
batch_learner: Renamed advanced_debugging to debugging_tools.
denoising: Renamed advanced_debugging to debugging_tools.
expanded_numpy: Renamed advanced_debugging to debugging_tools.
HDF5_importer: Renamed advanced_debugging to debugging_tools.
HDF5_logger: Renamed advanced_debugging to debugging_tools.
HDF5_serializers: Renamed advanced_debugging to debugging_tools.
neuron_matplotlib_viewer: Renamed advanced_debugging to debugging_tools.
neuron_volumina_viewer: Renamed advanced_debugging to debugging_tools.
read_config: Renamed advanced_debugging to debugging_tools.
simple_image_processing: Renamed advanced_debugging to debugging_tools.
tiff_file_format: Renamed advanced_debugging to debugging_tools.
wavelet_transform: Renamed advanced_debugging to debugging_tools.

This finally fixes issue #40.
HDF5_logger: Added the ability for HDF5ArrayLogger instances to overwrite values in the HDF5 file if specified so in the constructor.
batch_learner: Changed so that explicit deletion of intermediate data is not required.
batch_learner: Changed reading the original images to use the resume_logger.
batch_learner: Found a search that was not occurring in the right location in the HDF5 file.