Update manual for chunking changes from Mazin's Dissertation

[garfieldnate]

Notes from Mazin:

• The chapter in the manual on procedural learning is out of date.
  • Remove old terminology (DPKL, EBC, operationality) and update with current stuff from thesis
  • If the explainer were removed, the parts about it would also need to be removed.
• Add something about what is included in stats (for e.g. duplicates don’t increment anything). Why some numbers can be larger than totals.
• Add something to gds and chunking chapters that GDS does not monitor negative conditions

[garfieldnate]

Steven has approved the changes the changes_from_EBBS branch. However, the manual build is failing there because of some invalid links. Once that's complete, it'll be okay to merge.