+1 for vimwiki; all plain text, with some light organization sprinkled on top. I've gone the OneNote/Evernote/GoodNotes route and keep coming back to vimwiki. If I could find a non-kludgy way to get it on iOS, my grail will have been found.

You don't even need grep, as vimwiki has built-in search:

":VWS /pattern/

    Search for /pattern/ in all files of current wiki.

    To display all matches use |:lopen| command.

    To display next match use |:lnext| command.

    To display previous match use |:lprevious| command."