Update SCE file contents to include processed SCE objects

[allyhawkins]

Closes #93.

This PR updates the sce_file_contents.md section to include mention of the processed SCE object and any items that can be specifically found in the processed SCE object.

I made a few updates throughout here:

• I added a section below the colData tables discussing the presence of the ccdl_filter column that will be found in the processed objects. I mentioned briefly here that we do filtering, but not how the criteria are chosen. Instead I direct them to the processing information. The point I wanted to get across here is that there will be an additional column in the colData but they should all be labeled as Keep if they are in the processed object.
• I added any of the new changes that have been made to the metadata list for both the filtered objects and then the processed objects. I just added to the list and made a note if they were only found in the processed object.
• I added a new section for the dimensionality results. I kept it fairly short, but I didn't think it fit in anywhere else so included a brief discussion of what was calculated and how they can be accessed.

[allyhawkins]

I went ahead and updated this to include the correct contents for the filtered objects. I had forgotten that we re-write out the filtered object with the additional column and metadata. This should be ready for another look.

[allyhawkins]

I added another line that includes the filtering cutoffs and noted that the columns should be found in both the filtered and processed objects. Let me know if you had something else in mind.