Revert "add rm *.o to all the makefiles to make sure we dont suck in extra object files when making library archives"

This reverts commit a2b26edf621ec5c32cad05da2417e7e9b81d719b.
undo last change where we removed all the .o s since it turns out theyre important for gdb.  now we just remove them before making a library to serve the original porpose of not adding cruft from executables
Change how sequences are stored.  Keep only indexes and not lenghts on disk and move names into a separate array.  Version updated to 2 to reflect lack of backward compatibility
increase version in README
do not cache sequences until needed for the first time.  also keep names and coordinates in separate caches
Merge remote-tracking branch 'origin/development' into version2
reactivate preload of genome in lod manager because in version2 this should be fast
Merge remote-tracking branch 'origin/version2' into development
fix sonlib build dependency
ensure that all zero length sequences get added to both the position and the name cache (by storing them outside map)
remove some cruft
use columniterators tosite method to move around instead of creating new one each time.  not sure why this was taken out before. . hopefully i dont break anything
fix bug in last commit.  also scale probfrac when sequence length smaller than step
fix some checks on cahce size
fix bug in tosite where somehow the reference genome was incorrectly determined in weird cases
add some asserts
fix error when no sequence in genome.  this is a check that got broken in the v2 update
read in _totalSequenceLength from the sequence array if the DNA array is empty.  we want this to be valid even when the DNA is not stored to be consistent with last version
dont print empty sequences
add clearcache option to columniterators tosite method to guarantee that it lands on the desired column even in already visited.  update hallodgraph to use this option