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git submodules might break your simple method of deduplication.
packer supports 1. git repos, 2. luarocks (which in turn supports arbitrary installments and compiling of projects like luaformatter).
Also I dont see how plugins cant vendor their own makefiles to fetch dependencies, if necessary.
Plugins can vendor their own makefiles; submodules would cover a common use case for this and eliminate the need to manually specify e.g. run = 'make' for plugins which take this approach. It shouldn't interact with deduplication - plugins would be expected to structure their submodules such that any submodule dependencies are isolated and do not cause duplicate collisions (e.g. no adding submodules on a runtime sourced path).
re: YAGNI: Well, there's a reason I made this feature note almost a year ago and haven't prioritized implementing it 😄
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