Setting up files for rewrite

jslist.txt --  rationale and to-do file
Basic rationale: we want a single JS file that is organized well; this
will improve readability (organized) and caching (single file)

collector_1.0.0.js -- new js framework

oldJS.js -- all old JS pasted into one file (other files removed)
Timer and migrations

Created a new timer for things like form submitting and minTime
displays; fully documented with examples

Migrated most of the old code over; Have not yet migrated most of the
timer code as most will be replaced with calls to the new timer
function.
Adds 'show' functionality to timer

Sometimes it is helpful to show the timer (soTetris for example). This
adds a parameter to the timer function that allows you to specify a place
where the timer should display it's value.
Migrates StepOut JS, fixes timer bugs

Timer was previously offsetting itself if used as a callback for
itself. clearTimeout fixes this.
Timer would reformat the number patter on whole numbers. This adds an if
statement to append ".0".
Implements Instructions.php JS
Updates JS file references to collector_1.0.0.js
Migrates and implements more JS

All php files affected in this commit are functioning fully now
Updates all remaining JS except for multisession
Merge branch 'master' into js-update
Fixes bugs and cleans dead code