I think I understand your points and I surely agree with some of them. However, I am still not convinced about some of them and/or I have some comments.
A) The directory structure:
keeping all assets in one jar is very common practice for making a jar.
Indeed! But it only works for assets distributed together with the .jar and which do not change over time, it does not work for assets which do change over time or are added at user side.
Practically all the plug-ins I plan to make or have thought of fall in one or both of the above categories. I am sure the 'simple' scenario occurs too, but the structure has to accommodate plug-ins of any complexity and behaviour.
Regarding the elevator scenario, [...] Your instructions can say you can optionally make the subfolder and have the folder contain the config file and user provided model.
Oh no! Nobody reads instructions (except you, me and some other on this forum, of course... ), Windows users never pay attention to file/directory name case, everybody can make mistake... The less steps are required by the user and the most obvious each operation is, the smaller the probability of errors and problems. The simpler, the better; and "one plug-in, one directory" is hard to beat as simplicity and understandability.
And, in general, having each plug-in separated from any other and with all its components along it seems to me clearer, cleaner and easier to understand and to put into practice (incidentally, the requirement you seem to propose of .jar file name matching sub-directory name is another thing which can easily go wrong).
Placing the jar outside a subfolder makes it a bit easier to update jars (all jar files immediately under the plugins directory) or a way to quickly restore a plugin behavior (wipe the subfolder).
Yes, probably it makes easier to fix some errors; I believe that preventing or reducing errors in the first place would be better, though.
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B) Maven & NetBeans: I have never used either, as I'm in the Eclipse / Ant congregation (or :evil: , who knows...?), but I assume learning new tools is not an issue. In general, though, I would prefer if the plug-in specs define an intended result / structure, rather some specific way / tool / process to achieve it.
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C) Central repository/-ies:
C1: From the user perspective, as I said right above, one of the better ways to manage plug-ins would be if RW accesses and presents to user a list of installable plug-ins, to be downloaded and installed (and UNinstalled!) with the proverbial "single mouse click".
How the repository backing this list is organised, whether some quality control is assured or whether some requirements are made to appear in this list (and which ones), I believe are questions better left to the dev team to decide, according to the general application structure, dev resources and priorities, whether Steam (and Steam Workshop, in case) make requirements or assumptions and so on.
C2: From the plug-in developer perspective, a general repo for plug-in source code dev would surely be nice to have.
*) This can be as simple as a public github repo (which are free) or more structured (I don't think github public repos allows to restrict access to individual sub-directories).
*) It may be started and run by JIW (at several level of involvement depth) or it may an independent initiative (a few similar initiative already exist).
*) It may be totally independent from C1 (develop here and move to C1 when ready to ship), which would reduce the signal/noise ratio during development or it may be integrated in several ways and at several levels with C1.
As the "meat" of this repo would be largely supplied by the community (or by the pug-in developer sub-community), opinions / indications from JIW are important, but some kind of consensus from the (sub-) community should also be reached (maybe implicitly by participating or not to it).