Merge branch 'master' into barry/xcode

Added back usage of -saws_options to handle option requests with saws

Test code to use javascript solver guis with SAWs options handling

Merge branch 'barry/fix-complex-examples'

added PetscOptionsGetScalarArray() fixed a variety of examples with problems for complex scalar type

Merge branch 'barry/minor-draw-improvements' into jed/chem

Merge branch 'master' into knepley/feature-dmda-section

* master: (528 commits)
Doc: Fixed configure doc
Nightly summary: Added configure section.
TSSetErrorIfStepFails: fix __FUNCT__
TS: fi

Merge branch 'master' into knepley/feature-dmda-section

* master: (528 commits)
Doc: Fixed configure doc
Nightly summary: Added configure section.
TSSetErrorIfStepFails: fix __FUNCT__
TS: fix for TSGetRHSMats_Private() in the creation of the Arhs and Brhs matrices
protect logging of objects (which uses global variables) with PETSC_USE_LOG
error handler API had been previously changed but this example was not updated to new API.
DMPlex: Fixed bug in coordinate permutation
PetscSection: Doc fix for permutation
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bugfix of MatCreateSeqAIJFromTriple() contributed by Nicolas Marsic <nicolas.marsic@montefiore.ulg.ac.be>
bib: rename ref with duplicate key
Webpage: Corrected '-dm_mat_type cusp' to 'dm_mat_type aijcusp'.
completed removing server code that was not removed in previous commit
removed PETSc webserver and configure package files that supported it
Allow calling MatGetBlockSize[s]() before matrix preallocation
SNESLINESEARCHBT: Set the norms when exiting early due to negligible step.
fix outdated PetscOptionsList
SNESQN: only monitor real part of dot product (fails with C++ complex)
Fix for multiple definitions in mat/color/interface/ custom fortran bindings
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/da/dageometry.c
src/dm/impls/plex/examples/tests/ex4.c
src/dm/impls/plex/plex.c
src/dm/impls/plex/plexinterpolate.c

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Merge branch 'barry/saws'

Merge branch 'master' into barry/wirth-fusion-materials

Conflicts:
src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c

fix name for PetscOptionsFList() and get FList() and EList() working properly with SAWs legal values

using new SAWs_Selected() instead of trying to manage it with another published variable

changed -options_gui to -saws_options
made help message display in SAWs html page use PRE so it is well formated and allocate enough space to hold entire message

PetscOptionsSAWsInput() now properly publishes most options

converted uAMS usage to SAWs usage; starts server but cannot see any published directories

Merge branch 'master' of bitbucket.org:petsc/petsc

Merged petsc/petsc into rmills/petsc master

Merge branch 'barry/rm-xxxregisterdynamic' into jed/ts-eimex

PetscObjectComposeFunctionDynamic() and TSRegisterDynamic() were
replaced by PetscObjectComposeFunction() and TSRegister(), both of which

Merge branch 'barry/rm-xxxregisterdynamic' into jed/ts-eimex

PetscObjectComposeFunctionDynamic() and TSRegisterDynamic() were
replaced by PetscObjectComposeFunction() and TSRegister(), both of which
drop the string name argument.

* barry/rm-xxxregisterdynamic: (82 commits)
...

Conflicts:
src/ts/interface/tsregall.c

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Merge branch 'blaise/yaml'

* blaise/yaml:
yaml: remove trailing whitespace and avoid PETSC_OPTIONS in examples
yaml: makefile fixes for alltests
yaml: minor fixes: memory leak, match MPI types

Merge branch 'blaise/yaml'

* blaise/yaml:
yaml: remove trailing whitespace and avoid PETSC_OPTIONS in examples
yaml: makefile fixes for alltests
yaml: minor fixes: memory leak, match MPI types, update output/ex9_1.out
PetscOptions: Replaced the ugly if {} else if {} else if {} with a fancy switch statement in yamlimpl.c
PetscOptions: Added tests for PetscOptionsInsertFileYAML
PetscOptions: style compliance
PetscOptions: Add basic support for YAML-formatted options files

Conflicts:
src/sys/examples/tutorials/makefile

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Merge branch 'master' into jed/ts-eimex

Sync to include Git conversion, PETSC_EXTERN, and minor API changes.

Conflicts:
src/ts/interface/tsregall.c

PetscOptions: Add basic support for YAML-formatted options files

Basic support for YAML options files. This minimalistic parser does not
support advanced features (sequences, bookmarks), so it is re

PetscOptions: Add basic support for YAML-formatted options files

Basic support for YAML options files. This minimalistic parser does not
support advanced features (sequences, bookmarks), so it is really
a JSON parser.

Will try to add support for -options_file_type <TXT,YAML> flag in case
one want to add more options file formats in the future.

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commit after merge

Hg-commit: d45994b710e27c421e3a611629d33b9d321ce16b

Split out petscviewertypes.h

Fixes missing include in petscoptions.h that was impacting tests.

Hg-commit: 8bcec53e19497af1488dd5b8010346dc31f3f222

removed silly abreviations

Hg-commit: 0641f9ef776cf11cc3336b494981da756bf9d14f

Commit after merge.

Hg-commit: 7ae059cc471c053401c1d6a21c3e45b9d4418175

added appropriate #include to various synopsis in manual pages

Hg-commit: 649729772e487ab080652f3c9abb4b4203cfa79d