[galaxy-dev] tools version (eg: cufflinks) and bowtie indices file

Hi there 1. Why is it that even after installing cufflinks 2.1.1 from the toolshed, it doesn't get reflected when I clicked on the tool from the side panel? It still shows 0.0.5 and 0.0.7. Think it's the same with others too (eg: bowtie) 2. I've modified the bowtie_indices.loc file under tool-data but the entries doesn't get reflected on the Map with Bowtie for Illumina (select a reference genome). I did the same for the bowtie2_indices.loc file and this one got reflected under Bowtie2. Been a little frustrating. Can anyone please advise? Many thanks. Best regards liz