Each tiny module did just a bit more than it should have done or included just one more dependency than was necessary, sometimes the scope of the module would grow over time and all this added up. Also, different sub-modules used different sub-sub-modules for the same functionality so this caused a lot of duplication in the higher level modules.
For my own open source project, I've always been very careful about which dependencies I use. I favor module authors who try to keep their number of dependencies to a minimum. A lot of times, it comes down to figuring out the correct scope of the module... Most low level libraries should not need to do their own logging; therefore, they should not need to include sub-modules to colorize the bash output; instead, they should just emit events and let higher level modules handle the logging. Anyway there are many cases like that where modules give themselves too much scope.