Wysiwyg HTML - why Markdown?

I've been keeping a work journal on my thumb drive for a while now, and I've been using MarkdownPad to do it.   This is great because I can grep it, and I can edit it with a command-line editor and change anything.  I'm beginning to wonder whether I really need to do it this way.   Maybe I should author in HTML using a tool like KompoZer and index it with an HTML aware indexer.

Of course, I'm committed to the thumb drive - I'm employed by the Federal Government and using Github.com private is not enough.   Not even installing my own CMS (e.g. this site), is enough.  If I'm indexing this journal with DocFetcher, no code needs to be written to make that thing document-structure aware - DocFetcher is already HTML aware, and I can truly say that at least my Journal should never have to be viewed only through a text editor.    This is not the case with Markdown.   To have a Lucene based index of my Journal and continue to use Markdown, I'd have to write some code ;)