regex fix to match \r\n in wiki.php

updated regex to match \r\n as well as just \n, 
so md files created on win machines can parse json front matter.
fixed identical id tags in generated html

Generated html list no longer created multiple elements with an id of 'tree'
Now only topmost ul tag is given that id.
Merge pull request #21 from EightMinusEight/win_fix

Regex fix for md files created in Win