Add description of the Simulator UI

- added brief description of the simulator ui + images
- some minor modifications and notes in simulator .tex
- added biblio entries and cited them in the text 
- added brief description of the stimulus ui + image
- a few sentences about the scattered documentation
- a few notes
- added more biblio and included citations in the text
- added two figures showing the local connectivity kernel
- compiled new pdf (draft)
- changed indentations to tabs.