TSTrajectorySet: replace shell code with PetscRMTree() and PetscMkdir()

fix brackets and names

modify confusing names

change PetscFunctionBeginUser to PetscFunctionBegin

resolve conflict with master 2

resolve conflict with master 1

remove some whitespaces

adjust the scope of revolve macro

revolve configuration works

use macro PETSC_HAVE_REVOLVE

remove revolve sources files from PETSc

skip the starting and ending step correctly

color output messages

Use global stepnum only in the forward sweep, not in the recomputations stage

use global stepnum, and fix error types

remove printf statements (for debug only)

fix a tiny bug

two level checkpointing works perfectly; stupid revolve!

reduce number of checkpoints (the first and last ones are removed)

remove unneccessary if

fix the problem for ex9 which involves multiple TSSolve calls

refactor the code

change some names

add two-level checkpoiting, the version without revolve works

Postpone stack allocation to setup stage of tstrajectory, -tstrajectory_max_cps works now