Repository code organization needs improvement

[nyama8]

Structure of the qdl-utils repository is disorganized which complicates understanding and slows further development.

Current repository structure is:

qt3utils/
    hardware_type_1/
    hardware_type_2/
    ... [I.e. a list of various hardware types...]
    applications/
        controllers/
            [Random hardware controllers and YAML config files]
        application_1/
            [source code of various types]
        application_2/
    datagenerators/
        spectrometers/
        [Various application controllers]
    experiments/
        [Source code for epxeriments]

In this structure the main level of the repository is cluttered with various hardware types which are mixed in with other non-hardware subdirectories. Low-level hardware controllers are scattered throughout different parts of the repository due to conflation of the qt3utils.applications.controllers directory and the various hardware specific levels in qt3utils.hardware_type_X.

This will need to be discussed before committing to a final revised structure but I propose doing something along the lines of

qt3utils/
    hardware/
        hardware_type_1/    # e.g. `spectrometers` or `nidaq`
            [Classes for interfacing directly with the specific hardware 
             of type 1 (e.g. `andor` or `princeton`)]
        hardware_type_2/
            ...
        ...
    applications/
        application_1/
            config/
                [YAML config files, these are generally not shared between 
                 applications anyway?]
            [Source code files, possibly further separated into sub-directories
             e.g. `application_1/gui` and `application/controller` if complex?]
            main.py    # What actually launches the application
        application_2/
            ...
    experiments/
        [Source code for epxeriments]

With this structure, the low-level hardware controllers are separated and can be accessed straightforwardly by reference such as qt3utils.hardware.spectrometers.andor. Furthermore, this would completely separate specific applications and their components with hardware-specific code that is shared amongst different applications and experiments.

[nyama8]

After our discussion today, I will move forward with this reorganization process, more or less as described above. I might be able to update the name of the package as well to qdlutils in addition to cleaning up some of the existing code.

The aim of this process will be to rename and reorganize most of the base code. The first pull request will be after the names are changed.