Best practice for file management with multiple operations

When I previously used a different controller, I would cram all operations into one file. When I switched to LinuxCNC, one of the best pieces of advice I picked up on the forum was to break the operations into separate files, allowing an operation to be rerun or updated easily. This is great, but generating each file is sometimes tedious or error prone. Is is a good practice to generate a single file, with all the operations, but with each operation as a subroutine? If so, the work to modify the HSM post processor to do this is well worth doing to potentially avoid file management mistakes. Is there a better way to generate a single part file with the ability to jump to particular operations? I hope the question makes sense. I'm looking for advice on best practices. Sorry if this is a pretty basic question but I was not trained as a machinist.

Thank you, Kent

If the machine has a tool changer it makes sense to have everything in one file.

My machine needs manual tool change, and need to measure in every tool after change.
So I use a number of files, just named 1.ngc, 2.ngc etc. and load the next one when switching tools.
Sometimes, especially in the lathe, I split files between roughing and finishing in order to easily
rerun the finishing pass.

It may happen that a tool breaks in the middle of an operation. In that case I usually just rerun everything,
or I may edit out the already made portion, leaving the header lines intact.

I should say I only run one off, single parts.

Thank you. Sorry not to have mentioned that I do manual tool changes with offsets of all tools in the tool table, and I mostly do one-offs as well. For CAM I use Fusion 360 and Inventor HSM and am considering how to change the post processor for convenience. Alternatively, I'll leave the post alone, write out a single file per setup, parse the file in Python, splitting the file up into separate files based on tool change or operation number copying the preamble to each. Comments added in the CAM package could be used to control the splitting program. That's probably easier than modifying the post.

I too use Fusion 360 and have been into the post processor and modified. It isn't all that hard. At least after tinkering in it for a while.
When there are several operations with one tool I often select those operations and post them into one file. Typically Adaptive clearing followed by contour and horizontal milling in one go.

it is just a Time to spend to get a best practice
you can Edit the Postprocessor of Fusion to get to your needs
Maybe also a Full auto zero sequence with G38.2 if you like to do so

and you can start your G-code on almost every line in Gcode so M00 stop tool change and restart at the Given position

Fusion 360 and Inventor allow you to postprocess all operations or a sub-set, so I use that facility to make a file-per-tool. This means that I can easily tweak one op, or even switch that stage to a different tool if I discover all the 6mm cutters are broken.

This is very much a home-use hobby mindset though, production philosophy would be quite different.