Xavier,
May I suggest a slight reorganization of the "modules/{version}/init" folder.
I note that the contents of this folder, is the easiest way to get a list of shells that a particular version of modules supports.
First (and probably important), move profile.csh and profile.sh to a subfolder profile.d (and rename them modules.*).
This will make them easier to find and just use these by copying them to /etc/profile.d/
(I also suggest you put a test in those scripts that they are effectively noop if the user is root).
Next, rename the *_* and *-* files and folders to *.* - adding a .d to the folders (tcsh.completion, zsh.functions.d ) - or create a subfolder (maybe auxiliary.d, misc.d, or extra.d) for all of them. This part will make it easier to use the list of files to determine what shells modules supports (both by sight, and particularly in scripts).
Thanks.
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Paul FM Info: http://paulfm.com/~paulfm/
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