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