[Infrastructures] how to build an internal (local) file structure?

[Mike]

I don't like how previous administrators have set the internal,
home-grown scripts. Currently everything is just thrown into
/commands. What I want is to change the structure so that it
looks more like:

/COMPANY
  /bin
  /lib
  /etc

Like a typical unix box. My question is for things like data,
mapping, resource, or configuration files... where should they
go? If there is a file 'mapping.pl' that needs the file
'mapping.cfg', certainly the 'mapping.pl' goes in
/COMPANY/bin. Does the 'mapping.cfg' go into /COMPANY/lib,
/COMPANY/etc, or somewhere else?

What makes sense?

Mike