Get rid of the `ccdh-dev` fork of LinkML

[gaurav]

It looks like all the changes we've made in the ccdh-dev fork have been merged into the linkml main branch, except for the changes we made to markdowngen.py. In order to avoid having to maintain this LinkML fork, we should:

• Fork just the markdowngen.py file, which we will keep in the ccdhmodel repo. Ideally, make it easy to compare this file with LinkML's markdowngen.py so we can incorporate upstream changes easily.
• Update the Makefile to use our fork of the markdowngen.py when generating the Markdown generation.
• Add some tests to ensure that the Markdown generation uses features specific to CCDH.

[gaurav]

There's a new docgen in development that would allow us to use our own Jinja templates (linkml/linkml#498) -- that might make it pretty straightforward to do this!