rebuild the api manual since its been a while
fix typo
remove useless line to avoid unused variable warning on some systems
remove include of sonlib.  it doesnt seem like it was needed and was causing compiler warnings for some
add ucscNames option to hal2maf
essentially undo 9b19965bab9a1eee7e5c5040c75a64523e4c804d and 485ccf0c42fa67f58f54ea61a0cd7da519aacb02 which, by mucking with reverse coordinates, badly broke maf export and column iteration.  wish i could remember what on earth i was thinking as there must have been a reason
oops.  remove debug code that got accidentally committed
Merge branch 'development' into chains