Make `generate_references.py` configurable.

[1uc]

Adds the ability to customize with which flags nmodl is run to generate the references.

The default is "" (for CoreNEURON) and "--neuron" (for NEURON). These choices can be overridden by adding a file references.json to the usecase directory.

Since the logic is slightly more involved, the Bash script is reimplemented as a Python script.

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 86.24%. Comparing base (341b89e) to head (1db8b67).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #1286 +/- ## ======================================= Coverage 86.24% 86.24% ======================================= Files 178 178 Lines 13299 13299 ======================================= Hits 11470 11470 Misses 1829 1829 ```

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[bbpbuildbot]

Logfiles from GitLab pipeline #213713 (:white_check_mark:) have been uploaded here!

Status and direct links:

• :white_check_mark: spack_setup
• :white_check_mark: build:intel
• :white_check_mark: build:nvhpc
• :white_check_mark: test:intel
• :white_check_mark: test:nvhpc

[1uc]

Can be seen in use here: https://github.com/BlueBrain/nmodl/pull/1285 Direct link: https://github.com/BlueBrain/nmodl-references/commit/e26d23f160210bd5fc3b4fe68555cb1e2ac72e02