[Cppcms-users] How to Build Application Hierarchies Dispersed Across Filesystem

I'm slowly building a website that consists of multiple component apps,
each placed inside of their own root directory. The filesystem structure is
as follows:

(Assume "/" is the webserver root.)
Inside "/" is the top-level application, "klt".

Underneath root, we have the following directories:
/static/
/attach/

"/static/" is what you'd expect. Inside "/attach/", are symbolic links to
each sub-application's home directories, which holds templates, *.cpp and
*.hpp files, as well as the application binary and an application specific
config.js file.

How would I go about building everything into a single purpose application
hierarchy? I want each sub-application to be able to function completely on
its own as well as part of a unit. e.g. I can compile each sub-application
by itself and have it run on a web-server independently of the others. But
also compile the top-level application to include all the sub-applications,
and have them all work as a unit under "klt" app.

Do I try and compile all the templates from all applications at once? Then
compile all the app.cpp files together with their app_skin.cpp and
app_content.hpp files Do I have to specify the location of each cpp file
explicitly when compiling, since they are in different directories, and g++
wouldn't know where to look for them in that case?

Please note, that I'm in the process of debugging, and this is an old
project. So there's A LOT of other issues with compilation and linking that
I'm slowly working through. As a result, I can't test this directly and be
sure that any issues are with my build system's approach vs other issues in
the code directly.

So, before I spend huge amounts of time doing the wrong thing, I would like
to get some help about what the best way to build this setup actually would
be.

Additional Info:

1. My build system is actually currently pretty jank at the moment. I
eventually want to use autoconf. So any autoconf specific advice would be
helpful and appreciated.

2. Originally making sure each sub-application could function as a web app
on it's own was a high priority. That's no longer the case. So if it
actually would be far easier to just "dump everything into a single
directory", then I'm... willing to accept that. Though keeping things in
separate directories would also help keep things organized. So I'm not
entirely sure the best way to go.

Thank you very much for your time. :D