Well seems the right place since it is your winapi help topic of offline documentation
First Congratulations for jumping in and trying something. I've heard of PanDoc of course but don't have it. I also have the 'Helpwaregroup' tools but have not utilized it much as I refuse to download bloat.net for something to work so that limits FARHTML. Now unless these two tools are amazing, in which case I'm an idiot for not trying them, you have found you have a .chm documentation package using 250 Meg but with numerous unresolved issues.
You have done to the whole package what I did to just the Controls folder to test a method to get a complete working .chm help file. BTW I only have 660 links to fix before I rebuild Controls.chm
I would guess a number of things did not get done by those two programs. The biggest drawback might be the lack of the contents file which lists a treeview like structure of 'Books' 'Topics' 'sub books' etc. If FARHTML can import .hhc and .hhk files (it can see attachment, import of hhc from TOCYML) you can possible solve this deficiency by using the TOCYML tool at
https://forum.pellesc.de/index.php?topic=10571.0 to create the needed hierarchy for the contents file.
The TOC.YML file displays the correct structure of the contents file by indenting, but this not the representation that the .hhc uses. So TOCYML converts toc.yml to toc.hhc and toc.hhk structure. I'm fairly sure that if the toc.yml in each directory is converted, then the resulting .hhc files could all be appended together for a master .hhc which would be structured and created correctly for .chm. Same for .hhk. Haven't tried it but I think the worst case fix is that the header and footers need to be removed from files 'in between'. So I would modify TOCYML to accept two more switches /noheader and /nofooter.
The next thing to check did PanDoc or FARHTML rename all of the .md references to .html in each and every newly converted .html file? If they are still .md even if the syntax is correct for a link it is the wrong extension.
Well all for now as I seem to be writing a book ..... but there is more.
John Z
Today I will enhance ymltoc
The error message "The upload folder is full. Please try a smaller file and/or contact an administrator." prevents the attachment of FARHTML imported hhc file 52k picture ......
Update: New ymltoc works great to create hhc files that can be concatenated to create a single hhc. Need to test hhk too.
Update2: Works great! Both merged HHC and HHk files open and look correct in FarHtml and MS Help workshop.