Navigating Lisp data structures

[Matt <matt@excalamus.com>]

I'm writing an Emacs package and struggling to figure out how to represent the data in a Lisp data structure.  I'm getting lost in whether it should be an alist of alists, a plist of plists, an alist of plists, etc.  Or maybe it would be better to use a cl-struct or a hash or a class or a vector or a record.  Should I use keywords or not, etc.  

Here is a detailed explanation of my issue:

My Emacs package manages my project workflows (e.g. Python or C).  Each project has a name, associated files, one or more shell processes (comints), as well as commands for a specific shell and commands used across the shells.  It also sets my window layout.

In Python, I might structure the data something like this:

projects = {
    "my_c_project": {
        'shells': {
            "*build*": {"root": "/path/to/build/directory/", "setup": ("export MYBUILDVAR1=1", "export MYBUILDVAR2=0")},
            "*run*": {"root": "/path/to/run/directory/", "setup": ("export MYRUNVAR=1")}
        },
        'commands': ("./build_my_project.sh", "./run_my_build"),
        'files': ("/path/to/entrypoint.c", "/path/to/other/file/I/care/about.c"),
        'window_split': ("quad", ),  # C-x 3 C-x 2 other-window other-window C-x 2
    },
    "my_python_project": {
        'shells': {"*my_python_project*":  {"root": "/path/to/my/python/project", "setup": ("source venv/bin/activate")}},
        'commands': ("python3 -m my_python_project",
                     "python3 -m unittest discover tests/ --failfast --quiet", ),
        'files': ("/path/to/my_python_project/entry_point.py", ),
        'window_split': ("half", ), # C-x 3
    }
}

I could then get the information I need through chaining look ups.  If we pretended that Emacs used Python, activating a project might look something like this:

(Pdb) # create shells
(Pdb) for name in projects['my_python_project']['shells']: pass  # call comint creation command
(Pdb) # setup shell environments
(Pdb) for command in projects['my_python_project']['shells']['*my_python_project*']['setup']: pass  # pass each command in the comint
(Pdb) # load files
(Pdb) for file in projects['my_python_project']['files']: pass  #  run emacs find-file
(Pdb) # and so on

Of course the data could be represented using classes instead of dicts.  However, I hope the problem is clear.

I'm obviously looking at the problem through the lens of Python key-value structures.  When I try to translate the data structure to something like nested plists, it feels messy.  Maybe that's me simply being uncomfortable with nested lists?  When I mix list types (e.g. an alist of plists), the lookup syntax becomes inconsistent (a mix of assocs and plist-gets, scattered with cars and cdrs and weird cases in which I have a list of strings I can't seem to access).  

Guidance would be sincerely appreciated.