workflow-paper

I think Org-mode (in Emacs) does something similar to what you want. Here's link to page with add-on function to add drag'n'drop images to Org files. The web page itself is what was exported from Org, although the export could have as easily been to pdf. There's also link on this page to youtube video illustrating things: http://kitchingroup.cheme.cmu.edu/blog/2015/07/10/Drag-image... Org-mode itself uses its own rules for adding Markdown-like formatting, but Org-mode has features that go way beyond Markdown. Here's a fairly simple technical doc with a few images and footnotes: http://kieranhealy.org/files/misc/workflow-apps.pdf and here's the org file and images that you were used to author that document and export it to pdf: https://github.com/kjhealy/workflow-paper

That's not entirely true. org-mode is quite flexible and serves as a lot of things, and one of them is in fact as a TODO list [1]. This becomes particularly true when you use the TODO extensions. I am constantly surprised at the capabilities of org-mode. Some sociologists that I'm aware of actually generate their LaTeX publications through org-mode [2]. [1] http://orgmode.org/manual/TODO-Items.html [2] http://www.kieranhealy.org/files/misc/workflow-apps.pdf (generated through org-mode, source: https://github.com/kjhealy/workflow-paper)