use usual CommonJS directory structure
more work on using commonjs
mostly converted over to commonjs but haven't tested. still need to fix requires for pathCalculator shape files.
Update cross-platform-shapes.js
Rename ellipse-double.js to ellipseDouble.js
Rename endoplasmic-reticulum.js to endoplasmicReticulum.js
Rename golgi-apparatus.js to golgiApparatus.js
Rename line-catmull-rom.js to lineCatmullRom.js
Rename grid-square.js to gridSquare.js
Rename line-curved.js to lineCurved.js
Rename line-elbow.js to lineElbow.js
Rename line-segmented.js to lineSegmented.js
Rename t-bar.js to tBar.js
Rename sarcoplasmic-reticulum.js to sarcoplasmicReticulum.js
Rename line-straight.js to lineStraight.js
Rename rounded-rectangle.js to roundedRectangle.js
Rename rounded-rectangle-double.js to roundedRectangleDouble.js
Rename mim-transcription-translation.js to mimTranscriptionTranslation.js
Rename mim-binding.js to mimBinding.js
Rename mim-branching-left.js to mimBranchingLeft.js