Created attachment 213738 [details]
Sample files plus Doxyfile that demonstrate the bug.

Using markdown to generate lists improperly nests the 2nd - nth element in the list.  For example, the following:

 - item 1
 - item 2
 - item 3
 - item 4

Gets rendered as:

 * item 1
      o item 2
      o item 3
      o item 4

Same for numbered lists.  Also, a paragraph after a numbered list becomes the continuation of the last item in the list.

I have included three files as an attachment.  One is plain text, one is a python file and the last is C.  The plain text version doesn't have the improper nesting issue, but does have the improperly indented paragraph issue.  The python and C files demonstrate both problems.

I've included a minimal Doxyfile as well.