cleanup MatPtAP for mpiaij matrix; rm MatPtAP_Basic()
DMMesh: Now Overlap is also copied

--HG--
extra : rebase_source : 68701679a992690dd7bb6c0ec392ec361cb908aa
tried to add -ts_monitor_sp_eig but doesn't work with FD Jacobian
The logic in TS is too convoluted, we need to string out some cases and simplify
TSComputeIJacobian() doesn't work in monitor with FD Jacobian yet clearly does work
in the solver, why is that?
commit after merge
add -ts_monitor_sp_eig file
The current thread reduction model does not "wrap". modulo incompatible with guard above
Fix indexing bugs in VecMDot
Remove some unused variables from kernels
DMComplex: Reorganizing DMComplexCreateSection()
- Added DMComplexSetSubpointMap()

--HG--
extra : rebase_source : ec724d7984f13e092a83daf1058546a8adc1ad13
Small compiler fix

--HG--
extra : rebase_source : a1bbf497f3c5090a93635adc1e8ae8b2495d94d0
Minor fixes in website
started updating TS portion of users manual
Fix 43e28ef1a420 due to misplaced #endif

--HG--
extra : rebase_source : 0e3f0504d54141739a43f5b28e913afb37124611
add gmresr94 to petsc.bib
opensolaris: tighten __attribute((unused)) check

--HG--
extra : rebase_source : 99db96f5418b494be36cb1453023c776d4c0c84c
DMMesh: Another update to clone

--HG--
extra : rebase_source : 3acb2c71c1c1b62dbf80dadc17a3d19ecbb38592
DMComplex: Reorganizing treatment of boundary conditions
- Split up construction of default section
- Using ex31 as a test, with free slip boundary condition

--HG--
extra : rebase_source : 86feff6927be65a284d46bde0e76dbd872b13bf1
added a couple TS special cases to manual
changed state vector x to u in ts.c
fixed formating of variable declarations in ts.c
add MatPtAP_SeqAIJ_SeqMAIJ() to be consistent with changes made on MatPtAP_xxx
rm MatOps 98-101: MATOP_PTAP_xxx_aij - these are actural implementations