are there any libraries that can convert a kotlin source directory into a... virtual heirachy tree complete with full source code information such that the source code is embedded with the information itself

That is called kotlin compiler. If you are writing plugin for IDEA it is very easy to access and manipulate PSI nodes (that is how all the inspections and refactorings work)

i basically want to embed my applications source code into a class that it then uses at run time

maybe there is a classloader magic way to do this, but generally I'd say "no, not possible" to this. Kotlin is a compiled language, not interpreted.