UI of Rename button in Author mode

Done UI of Rename button and pop-out widget.
Fixed transparent bottom for both Rename and Description.
Order descriptions, inputs and units(unfinished)

The descriptions and inputs have been re-ordered alphabetically. The
units haven't.
Order descriptions, inputs and units done

The descriptions, inputs and units have been re-ordered alphabetically.
Merge branch 'master' into jingxian2
Order name, desc, inputs and units in Author done

In AUTHOR mode, the name, descriptions, inputs and units have been
re-ordered alphabetically.
fix indentation and whitespace
Root node selector relocated

The "root" checkbox is now in a individual row between "type" and
"inputs".
Midpoint addition

Added midpoint formula to integrate.js as well as a testing function to
integrate.html
changed gitignore
Midpoint method integration

Added midpoint method to calculations.js
Added getter to model.js
Added option to use eulers or midpoint
Midpoint is currently the default option for testing
Fixed issues to test midpoint

Fixed issues with setting integration method as a parameter so that I
could do some system tests with the midpoint method
Merge branch 'master' into jingxian2
Added more time options

Added seconds, minutes, days and weeks to the time options in author
mode and put them in order of increasing length
Uncommented euler midpoint switch logic

Changed this out of a comment and got it working with both methods
Ignored dojo
Merge branch 'master' into dillanButler
renaming/resaving  problem in author mode
renaming problem , clone method added for copying parameter object
reusing save problem for save As
Merge branch 'master' into pradeep