Ideally each new point should be a separate PR on its own but it was too intertwined to separate when I was done with writing.

No problem! As long as the code is improving we won't face such issues in the future.

Need much testing here as I do not have sheets with markers

Yeah, they were updated into sample1 folder. I will test by updating their template.json files (might need a bit help from you here)

Not sure which name fits so I just called them extensions for now

modules would be a better term I think.

Not sure if template is the best place to specify preprocessors

Yes, template.json shall not contain the whole preprocessing config. At-least there should not be a compulsion to supply it in every template(As it is not the user's worry). Also, the --noMarker flag, etc would have an alternative through this, might increase confusion on using both.

Maybe we should differentiate between template and configuration file.

Valid point, maybe an additional config.json file which if present, will override the default config including preprocessing and the flags.

And it is confusing to keep wondering what case the keys are.

We can follow camelCasing for all keys, lowercase would cause readability issues.

Next step should be to clean up the output file paths.

Would look into it :)

This branch would contain my changes(conflict resolutions and sample case fixes etc) over your commits for merging this PR with conflicts-
https://github.com/Udayraj123/OMRChecker/tree/leongwaikay-extension-framework

@leongwaikay just giving update - I will soon find some time to finish reviewing this PR(with a fabulous contribution of +1000-400). Thanks for being patient!

@leongwaikay I am currently testing out my samples with the new configurations. Specifically, using the Markers.py extension(now renamed to CropOnMarkers.py) with sample1.
I see that getBestMatch(...) from utils.py is not yet ready to accept the new ImageProcessor.

Exception has occurred: AttributeError
module 'config' has no attribute 'marker_rescale_range'
  File "/OMRChecker/utils.py", line 267, in getBestMatch
    config.marker_rescale_range[1] - config.marker_rescale_range[0]) // config.marker_rescale_steps
  File "/OMRChecker/extensions/CropOnMarkers.py", line 78, in apply_filter
    best_scale, allMaxT = utils.getBestMatch(image_eroded_sub, self.marker)
  File "/OMRChecker/main.py", line 332, in process_files
    inOMR = pp.apply_filter(inOMR, args)
  File "/OMRChecker/main.py", line 85, in process_dir
    process_files(omr_files, template, args_local, output_set)
  File "/OMRChecker/main.py", line 93, in process_dir
    process_dir(root_dir, d, template)
  File "/OMRChecker/main.py", line 93, in process_dir
    process_dir(root_dir, d, template)
  File "/OMRChecker/main.py", line 582, in <module>
    process_dir(Path(root), Path(root), args['template'])

Will fix this so that Older samples also get compatible with this configuration

Edit: Fix added(with many other changes for making sample1 run) :-4cdc4fe

@leongwaikay I have made changes in your branch to make it compatible with my samples.
Edit: Merged now. Cheers!