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
remove erroneous error when bed end coordinate is equal to sequence length.
fix indento
Revert "fix indento"

This reverts commit 720ca26b7a1522f6a018ea7af58b0e972b54e6cf.
fix indento
change sed option order to work on mac too
try changing each maf to ss before affregating
fix sonlib build dependency
fix sonlib build dependency
add noAncestors option
fix other indent error i think
ensure that all zero length sequences get added to both the position and the name cache (by storing them outside map)
remove some cruft