updates to TSAdjoint users manual documentation and related manual pages
to make things more consistently and clearer

cleanup of TSAdjoint manual pages and notation for function arguments

improve docs for TSSetFromOptions

TS: Added -ts_fd_color to compute an IJacobian with coloring

TS: Added Matt's braindead IMEX method for debugging
- I can't get any of the PETSc IMEX to work at all
- Its named MIMEX
- It just solves the implicit part, and then takes an explicit step

Merge branch 'master' into knepley/feature-harmonic-advection

* master: (205 commits)
Bib: Added bio refs
Don't print SAWs URL since it disturbs all the test output
missing (double) cast in pr

Merge branch 'master' into knepley/feature-harmonic-advection

* master: (205 commits)
Bib: Added bio refs
Don't print SAWs URL since it disturbs all the test output
missing (double) cast in print statement
don't output to test file all 12 digits of values
fixes and additions to SNESQM manual pages
PetscViewerBinaryGetDescriptor() is now a collective and must be treated as such fixed some calls to PetscViewerBinarySetUseMPIIO() removed some test runs that take too long
removed dead routine
ViennaCL: Added MCS download mirror URL for version 1.6.2
shift order of processing options for TS to be compatiable with SAWs Fix options handling for SAWs to duplicate array that previously was deleted too soon for SAWs processing
remove some dead code for AD and old AMS java and Matlab utilities
add missing PetscFunctionBegin; that messed up displaying of stack
Viewer: Fixed PetscViewerBinarySetUseMPIIO() in some examples
removed unused variables, removed dead code from AMS
git is so freaking annoying I accidently made a bunch of updates in next which I pushed lets see if this diff makes the same changes in my branch Why can't git just forbid me to make changes or next or set up some utility to prevent it!
moved saws directory to proper share directory location updated source to point to it.
rm checkboxes at top of pcoptions.html (ugly and not useful) and centered display of solver
PetscOptionsObject->prefix was freed before using in SAWs post processing hence SAWs was unable to change any type which had a prefix
display URL to point to to access SAWs server
missing break in case for handling string arguments better description for Options database option handling
removed extern PC_CLASSID and KSP_CLASSID that don't belong in petscoptions.h
...

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TS: In order to make things work with Vec viewers in TS monitors, I needed to set the initial sequence number

Merge branch 'barry/saws-options-merge-master'

removed dead routine

shift order of processing options for TS to be compatiable with SAWs
Fix options handling for SAWs to duplicate array that previously was deleted too soon for SAWs processing

Merge branch 'maint'

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c
src/sys/threadcomm/interface/threadcomm.c

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Merge branch 'tisaac/simplify-register-all'

Removed the XXXRegisterAll() functions from the public interface. These should now only be handled by the package intialization functions.

TS: Use %g to draw time in TSMonitorDrawSolution()

Merge branch 'barry/petsc-sa-refactor-rebase'

VecViewFromOptions() must be called on solution, not u since u may not have been passed in by user
TSStep() should NOT be calling VecViewFromOptions() because it is treating it as a monitor, not a -x

VecViewFromOptions() must be called on solution, not u since u may not have been passed in by user
TSStep() should NOT be calling VecViewFromOptions() because it is treating it as a monitor, not a -xxx_view
TSStep() manual page should reflect the fact it is not to be called by users except under very limited circumstances
missing CHKERRQ() in example

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fixes for manual pages for TSSetRHSJacobian()

Reported-by: Mark Adams <mfadams@lbl.gov>

removed unused variables in bus adjoint examples
fix uninitialized variables issues for adjoint solver

fix for manguled manual page

Reported-by: Peter Lichtner <peter.lichtner@gmail.com>

removed q argument to TSAdjointSetCostIntegrand() since can be created automatically

drop the P from TSAdjointSetRHSJacobian() remove C++ commments from adjoint examples

merge TSAdjointSet/GetSensitivities[P] into TSAdjointSet/GetGradients

remove need to call TSSetDuration() for TSAdjointSolve() and introduce optional TSAdjointSetSteps() for integrating backwards less than the full number of steps

remove user.shift from ex9bus user context that is never needed

remove solution vector from calling sequence of TSAjointSolve()
change Quadrature name to Integral to match use of Integrand name and clarity to users for TSAdjoint