Allow bytecode enhancement to update analysis

This breaks the loading/saving of the incremental compiler analysis out
into separate task, thereby providing the necessary hooks for byte code
enhancement tasks to enhance bytecode and update the analysis before the
analysis gets stored to disk.
Deprecating old APIs and attempting to document behavior correctly.

* Removed as many binary incompatibilities as I could find.
* Deprecating old APIs
* Attempt to construct new nomenclature that fits the design of Incremental API.
* Add as much documentation as I was comfortable writing (from my understanding of things).
Tweak remaining binary compatibility issues with design.
Debug issues with implicit usage for CompileSetup.

* Force CompileSetup Equiv typeclass to use Equiv relations defined locally.
* Add toString methods on many of the incremental compiler datatypes.
* Remove remaining binary compatibility issues in Defaults.scala.
Fix scripted test to understand new compile/compileIncremental task switch.
Adding more scaladoc to incremental compiler library.
First set of refactorings from review.

* Split Java analyzing compile into its own class.
* MixedAnalyzingCompiler now only does the mixing
* Start moving methods around to more-final locations
* Static analyzingCompile method now constructs a MixedAnalyzingCOmpiler and delegates to incremental compile.
Finish rearchitecting.

* IncrementalCompiler IC object now holds the actual logic to start incremental compilation (rather than AggresiveCompiler or other)
* MixedAnalyzingCompiler ONLY does anlaysis of Java/Scala code
* Moved the AnalyzingJavaCompiler into the integration library so that necessary dependencies are visible.
Fixes @eed3s1gn's comments

* Use verbs.
* compile actually saves the analysis
* previousCompile loads previous anlaysis
* explicit task to override for bytecode manipulation folkel.
Merge pull request #1714 from sbt/wip/bytecode-enhancement

Expose mechanism whereby bytecode enhancement can be run *before* saving incremental compiler hashes.