Add CLI to create flattened composite images

[tieneupin]

Adds an additional command line interface to allow users to manually merge grayscale images from different colour channels in a dataset to create a composite image.

This pull request introduces the minimum features needed in order to create such a composite. More features will be added in future pull requests.

[tieneupin]

@d-j-hatton , @stephen-riggs , I've tested the CLI with flatten both enabled and disabled, and it successfully produces 2D and 3D images. Currently, it can run into memory allocation issues when flatten is disabled due to the size of the stacks we're dealing with, so it might be worth considering packaging it for users as a cluster job instead.

[tieneupin]

Validation tests done:

• clem.lif_to_stack CLI works
• clem.tiff_to_stack CLI works
• Cluster submission of LIF processing job works
• Cluster submission of TIFF processing job works
• clem.process_stacks CLI works

[codecov]

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