obsidian-extract-url VS longform

There is the extract-url plugin, that works with web links. I don't know if it can work with internal links too.

Otherwise, even if it is a bit convoluted, the longform plugin can be used to compile a collection of different notes in a single "manuscript". Just create a longform project and have one card per file, then you compile them.

The longform plugin is all about taking individual notes for chapters/snippets/etc in a single project and putting them together.

Depending on your usecase you could try longform plugin to compile and export multiple files as pdf.

In addition, if you'd like to split your long Markdown file into separate files (one for each chapter, or whatever structure your academic writing has) you could look into the Longform plugin. It can merge multiple files (and do a lot of other stuff, like removing links etc), and then you could add the Pandoc conversion as a final step in the Longform workflow. https://github.com/kevboh/longform

It might not be exactly what you're looking for, but it is free and it's all local. If you decide to give it a go, try a few of the community made plugins (I use Longform, Advanced Tables, Templater and Tracker) to see just how cool and easy it is to customise. Installing directly from the community plugins browser isn't the most secure, but you can manually install whatever you want just by downloading directly from GitHub. It's a lot easier than it sounds!

The longform plugin is pretty nice, turning Obsidian into a Scrivener-esque tool for writing individual bits that can be drag-rearranged in the project pane view, with the added benefit of being able to use Obsidian's easy cross-linkings.

The Longform plugin will get at both things, admittedly in relatively kludgy way. It treats specific folder-bound sets of notes as scenes in a draft, and those scenes can be manually dragged to reorder them, then a compile action can stitch them all together into a new note. The default compile steps strip links and such, but you can make a custom sequence that just retains the stitching together while retaining all markdown formatting.