Perhaps one of the biggest drawbacks of Evernote (and OneNote) is that they both require you to trust that they are not doing naughty things with your data and I don’t. The best combo I’ve found so far has been Atom + Pandoc Markdown Plugin + Pandoc. Rendering my markdown is a pain – the Atom plugins for this are not perfect and due to different flavours of markdown and rendering engines, I can render the notes in one tool and find that they render completely different in another.
That one plugin, as good as it is, doesn’t solve all my other gripes though. There is a really good atom plugin for this that allows you to “paste” images in your clipboard buffer into your notes and will automatically save it to disk and generate a link. My assets tend to get very fragmented in this case too because I might use the same image in multiple notes and end up storing multiple copies of it in different “assets” folders. Inserting images into markdown notes is a pain because I need to download the image, place it in a folder relatively near to my content and add an image markup section to my code.Searching for notes in markdown requires me to read the grep man pages for the umpteenth time because I’ve forgotten which flag to set to turn on or off regex in the particular flavour I need.
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