Commits for braney

v309_preview2 to v309_base (2014-11-17 to 2014-11-24) v309

• chains are filtered on normScore
  • src/hg/hgTracks/chainTrack.c - lines changed 2, context: html, text, full: html, text
• make sure that description HTML ends in .html, but not twice. #13516
  • src/hg/lib/trackHub.c - lines changed 6, context: html, text, full: html, text
• backout change to allow gff3 files to not specify phase on exons (perMark)
  
  • src/hg/utils/gff3ToGenePred/tests/expected/errCases1Test.out - lines changed 6, context: html, text, full: html, text
  • src/lib/gff3.c - lines changed 1, context: html, text, full: html, text
• when hubs disappear out from under us, put out a kindler, gentler errormessage that gives people a clue what's happened. #14365
  
  • src/hg/hgGateway/hgGateway.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgTables/mainPage.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 2, context: html, text, full: html, text
  • src/hg/inc/cart.h - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/cart.c - lines changed 22, context: html, text, full: html, text
  • src/hg/lib/hdb.c - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/hubConnect.c - lines changed 3, context: html, text, full: html, text