I've given up about 4 months ago and switched to an IDE project in Git repository.
Registered at CloudHQ and set up a sync to Google Drive https://www.cloudhq.net/synchronize/evernote/google_docs
Downloaded the files and made an Intellij IDEA project out of them.
Created a free private Git repository at https://bitbucket.org
copy project there
for cool markdown highlighting https://plugins.jetbrains.com/plugin/7896-markdown-navigator
for clickable links https://plugins.jetbrains.com/plugin/40-hyperlink
And now I have:
beautiful markdown highlighting
full linux support
backup in multiple places
ability to open notes in text editor, e.g. Sublime
all the IDE power at my fingertips:
search files or in files, or in directory, or in search results - Regex, match case, file mask, group results...
notes structured into directories
running snippets or even ansible scripts to setup whole system
using variety of plugins...
Thank you so much Evernote, I don't know how I lived without all this