Hello @tommyf,
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About your First Question
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Do the token registrations get stored within the project files themselves or do they get stored in local machine or user settings for c4d. Meaning that if we wanted to implement this for our render farm we'd have to register the token on each one of the machines.
Implementing a custom render token can be done with our C++ or Python API (here is an example for Python). So, you will need such plugin on each machine where you want to use that token. Not quite sure how the rest of your question is meant, 'registering a token (or any other plugin)' just means that the plugin is present when Cinema 4D is booting.
Depending on how 1 is answered is it possible to support multiple $frame padding configurations?
Since you do not explain what you would consider '4 to 6 digit frame padding', I can only speculate. My guess would be that you want to replace the frame counter provided by Cinema 4D in file names, e.g., transform my_render_001.tif, my_render_002.tif, etc. into my_render_0001.tif, my_render_0002.tif, etc.
If that is what you mean, then no, that is not possible with tokens. The frame counter is something added by Cinema 4D you cannot influence as a user (as it depends on the render settings).
You could either implement a token which adds your own frame counter to a file name (my_render_frame-0001_001.tif, my_render_frame-0002_002.tif, etc.) or you could write a postprocessor which hooks into MSG_MULTI_RENDERNOTIFICATION to catch a finished rendering and then post-process the files it created on disk. But the latter could get complicated.
Also depending on how 1 is answered, are the token registrations permanent or are we going to have to register the custom token every time we launch c4d or whenever we want to change it.
As explained above, I do not really understand what you are asking for. A registration is not something you do manually as a human, but rather some code that runs.
Cheers,
Ferdinand