Polish up Tools section

[samm82]

TODO

• Do surface-level pass through Augmented Flaw Analysis for passive voice, past tense, etc.
• Deduplicate code for example glossary tables with Python script
  • Read in the actual CSV files used to make the graphs associated with these tables
• Add grey-colored node to legend of Fig. 3.1
• "Summarize all the data … [I track,] all the possible relations between the data, and the modifiers for those relations" (see Feedback on Tools (formerly Methods) Section #93)
  • Note the significance of "rigidity" when applicable (i.e., ensure I include a pointer to its definition)

I may also need to formalize how these tools actually work (maybe via pseudocode of my script[s]?) if needed (#149 should shed some light on this).