Remove intermediate _clustered/_consensus directories/files from pixel and cell clustering pipeline

[alex-l-kong]

What is the purpose of this PR?

Closes #571. There is no need to create a separate pixel_mat_clustered directory/cell_mat_clustered file as the data is just the channel expression/pixel cluster count expression values with an additional pixel_som_cluster/cell_som_cluster attached. Ditto for the pixel_mat_consensus directory/cell_mat_consensus file. These should be removed from the pixel and cell clustering processes.

How did you implement your changes

We should overwrite the original data with the newly created data in the cluster_pixels/pixel_consensus_cluster (and similarly for the cell clustering functions).

Remaining issues

There are a few extra checks we need to include for validation if the user decides to rerun the clustering pipeline in the same session.

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[alex-l-kong]

This branch is almost done, need to verify the outputs match up compared to the original.

[ngreenwald]

This looks great. Did you already run both notebooks on the HIV dataset to check that everything is working?

[alex-l-kong]

@ngreenwald yes, I'm currently running one more test to be sure.

[ngreenwald]

Looks good, just one leftover path change in the notebook

[ngreenwald]

Looks like some merge conflicts from the normalization PR I just put in

[alex-l-kong]

@ngreenwald resolved