refactor: create helper function for code regeneration

[maelle]

Related to #742

Questions

• what other files can be regenerated
• should there be a special value of file for regeneration all of them (NULL)

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[krlmlr]

This is showing weird

fatal: detected dubious ownership in repository at '/root/workspace'

errors when run.

Why do we need an R wrapper for a shell call?

We can work together on cleaning up the process and the documentation.

[maelle]

Why do we need an R wrapper for a shell call?

I thought it'd be smoother (since I am mostly working in the R console) but if it's not possible, I'll keep using the shell call.

[krlmlr]

Need to look at the error messages together.

[krlmlr]

We no longer run make in Docker, instead the Makefile contains docker run instructions.