added itis-api man file for all low level itis fxns
moved old phylomatic tree 2 vers to inst/ignore
fxns tp_classification now defunct #381
fxns eol_hierarchy now defunct #381
fxns col_classification now defunct closes #381
updated deprecated and added defunct man files
tpl_search now defunct, #381
marked 6 fxns as deprecated #281
added internal use of .deprecated to deprecated fxns #281
updatded deprecatd fxns manual page for note about traits package, #281
updated pkg level man page to indicate soap changes
fixed pkg level man file link error
fixed calls to defunct
bumped date and patch ver
removed @ method lines from classification fxns as not needed
changed classification fxns to do return_id by default, #380
return_id true by default, fixed downstream use in rbind and cbind and for ids extension class closes #380
added switch to synonyms to dispath to different sources #383
fix in clasisifcation to use call. instead of .call in stop call
fix in children fxn to use call. instead of .call in stop all