Editing preferences topics for clarity

Adding context sentences to topics to locate and explain the settings
and what they affect.
General edits for clarity.
Removing duplicated content.
Updating profiling colors and styles config

But see issue #46
Editing preference topics for clarity

And fixing a few other issues along the way.,
Addressing Radu's point from issue #46
Addressing issue #47 -- mathflow support in Eclipse
Fixing some of the mess I made related to issue #46

A number of outstanding issues remain relating to issue #46. The current
content does not fully describe the behavior as I currently understand
it.
Editing configuration topics for clarity

Plus some others encountered along the way.
Merge branch 'dev'

* dev:
  Editing configuration topics for clarity
  Fixing some of the mess I made related to issue #46
  Addressing issue #47 -- mathflow support in Eclipse
  Addressing Radu's point from issue #46
  Editing preference topics for clarity
  Updating profiling colors and styles config
  Editing preferences topics for clarity
Remove project file from .gitignore.
Fix validation: exclude note from developer deliverables.