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Write your own? I'm sorry but if Bundler doesn't solve your problem (or introduces other problems) either try and fix those issues OR write your own dependency management lib.
The unfortunate reality about writing your own new Bundler is that you'll inevitably end up rewriting Bundler. Isolate is basically just a mini-Bundler with a different (arguably simpler) storage location, but the storage location is really not where the complaints about Bundler are coming from. Rewriting things just to shed complexity or "bloat" will often just put you in a position where your library just can't do…
Any open source project needs help. The maintainers of Bundler have 200+ issues on the issue tracker. If people could help them replicate and confirm issues, write failing tests and if possible write patches ― it would do a world of good. But instead it's EASIER to complain and whine. So...