Initial CRA turnin.
The code is based on the opencoho codes, with only reachabilty analysis
codes. Some comments and exampels added. Config and flow are re-orged.
The m2j.log is required for install.sh
remove not used files
add bin dir
update install.sh to generate cra_info.m which is not in the repo
fix the calculation error in the 3vdp model. sovled the problem finally
 Committer: Chao Yan <chaoyan@cs.ubc.ca>
	deleted:    Projectagon/test/debug_disjoint_projs.m
	modified:   Projectagon/test/test_ph_forward.m
	modified:   install.sh
add comments to projectagon test, update install.sh

modified:   test_ph.m
modified:   test_ph_forward.m
modified:   ../../install.sh
comment out assertions which could fail because of computation error
	modified:   Polygon/poly_interval.m
	modified:   Projectagon/Forward/ph_advanceSafe.m
	modified:   Projectagon/test/test_ph_forward.m
1 change the name from concave projectagon to non-convex projectagon
2. update the 3vdp example to measure the performance
	modified:   Polygon/poly_contain.m
	modified:   Projectagon/Forward/ph_advanceSafe.m
	modified:   Projectagon/Forward/ph_getOpt.m
	modified:   Projectagon/Ph/ph_canon.m
	modified:   Projectagon/Ph/ph_contain.m
	modified:   Projectagon/Ph/ph_convert.m
	modified:   Projectagon/Ph/ph_create.m
	modified:   Projectagon/Ph/ph_intersect.m
	modified:   Projectagon/Ph/ph_intersectLP.m
	modified:   Projectagon/Ph/ph_interval.m
	modified:   Projectagon/Ph/ph_regu.m
	modified:   Projectagon/Ph/ph_union.m
	modified:   Projectagon/test/test_ph_forward.m
ph_verify may fail because the ph_simplify may make the real bloat amount much larger, so ignore the verify failures now.  both 2sink and 3vdp passed!

	modified:   Forward/ph_advance.m
	modified:   Forward/ph_advanceSafe.m
	modified:   test/test_ph_forward.m
Add doc for projectagon package. Leave CRA_HOME in matlab search path to call cra_open again.
	new file:   Projectagon/readme
	modified:   cra_close.m
Add readme for INT packages. Remove bugs test in the test func. Update the comments in int_forward accordingly.
	modified:   Integrator/int_forward.m
	new file:   Integrator/readme
	modified:   Integrator/test/test_int.m
clean the utils packaggges: a) remove non-used functions b) add test
	deleted:    Utils/BoundingBox/bbox_intersect.m
	deleted:    Utils/BoundingBox/bbox_neg.m
	deleted:    Utils/BoundingBox/bbox_sub.m
	deleted:    Utils/BoundingBox/bbox_sum.m
	deleted:    Utils/BoundingBox/bbox_union.m
	deleted:    Utils/Preprocessor/proc_file.m
	deleted:    Utils/Preprocessor/proc_macros.m
	deleted:    Utils/test/sample.m
	deleted:    Utils/test/sample0.m
	deleted:    Utils/test/sample1.m
	deleted:    Utils/test/sample2.m
	deleted:    Utils/test/sample3.m
	deleted:    Utils/test/test_log.m
	deleted:    Utils/test/test_proc.m
	deleted:    Utils/test/test_struct.m
	new file:   Utils/test/test_utils.m
	deleted:    Utils/utils_combineInd.m
	deleted:    Utils/utils_decompDouble.m
	deleted:    Utils/utils_hashtable.m
	deleted:    Utils/utils_palette.m
	modified:   Utils/utils_struct.m
	modified:   install.sh
Add readme
	modified:   install.sh
	modified:   readme
more comments to the example
	modified:   test_ph_forward.m
forget the enable the 3d-vdp example
	modified:   test_ph_forward.m
update HA interace
1. state
  merge all function calls to callBacks.
  rename and recode ha_funcTemp to ha_callBacks.
  add tubes & comptime to ha_stateReach.
  support gate 0, which is the reachable region.
2. trans
  change transAct to resetMap.
	new file:   ha_callBacks.m
	modified:   ha_create.m
	deleted:    ha_fastStableState.m
	deleted:    ha_funcTemp.m
	modified:   ha_reach.m
	modified:   ha_slice.m
	modified:   ha_stableState.m
	modified:   ha_state.m
	modified:   ha_stateReach.m
	modified:   ha_trans.m
	modified:   ha_transState.m
	modified:   test/test_ha.m
	modified:   ../Projectagon/Forward/ph_advance.m
	modified:   ../install.sh
check other ha files. to be tested
dosn't support a cell of functions for sliceCond. so need to update
ha_slice. Maybe remove the ha_slice function?
	modified:   ha_slice.m
	modified:   ha_state.m
	modified:   ha_stateReach.m
Fix several bugs.
remove ha_slice to simplify the current code. It's not used by CRA
itself. Maybe useful for circuit modeling. Then add it later.
	modified:   ha_callBacks.m
	deleted:    ha_slice.m
	modified:   ha_stateReach.m
	modified:   test/test_ha.m
	modified:   ../Projectagon/Ph/ph_create.m