fix some markdown in CHANGES.md and add some more PR refs (#1732)

this also now makes the changelog part of the docs with links to the PRs.

Author: zingale

.gitignore

@@ -80,7 +80,7 @@ extern.f90
 build/
 doxy_files
 Docs/source/runtime_parameters.rst
-
+Docs/source/changelog.md
 
 # C++ parameters
 extern_parameters.H