bin run.rb

# file bin/run.rb
require 'bundler'

Bundler.setup

puts 'hello2'

p Gem.loaded_specs['json'].require_path

Gemfile

source 'https://rubygems.org'

gem 'json', '1.8.3'

gem 'warbler', :group => 'development'

shell output

$ warble
skipping json (/Users/cmeier/.rbenv/versions/jruby-9.1.0.0-dev/lib/ruby/gems/shared/gems/json-1.8.3-java does not exist)
No executable matching config.jar_name found, using bin/run.rb
rm -f json-bundler-warbler.jar
Creating json-bundler-warbler.jar

$ java -jar json-bundler-warbler.jar
LoadError: no such file to load -- bundler/dep_proxy
  block in expand_dependencies at uri:classloader:/gems/bundler-1.12.3/lib/bundler/definition.rb:630
                          each at org/jruby/RubyArray.java:1593
  block in expand_dependencies at uri:classloader:/gems/bundler-1.12.3/lib/bundler/definition.rb:629
                          each at org/jruby/RubyArray.java:1593
           expand_dependencies at uri:classloader:/gems/bundler-1.12.3/lib/bundler/definition.rb:626
         converge_locked_specs at uri:classloader:/gems/bundler-1.12.3/lib/bundler/definition.rb:594
                       resolve at uri:classloader:/gems/bundler-1.12.3/lib/bundler/definition.rb:195
                         specs at uri:classloader:/gems/bundler-1.12.3/lib/bundler/definition.rb:140
                     specs_for at uri:classloader:/gems/bundler-1.12.3/lib/bundler/definition.rb:185
               requested_specs at uri:classloader:/gems/bundler-1.12.3/lib/bundler/definition.rb:174
               requested_specs at uri:classloader:/gems/bundler-1.12.3/lib/bundler/environment.rb:19
                         setup at uri:classloader:/gems/bundler-1.12.3/lib/bundler/runtime.rb:14
                         setup at uri:classloader:/gems/bundler-1.12.3/lib/bundler.rb:95
                         <top> at uri:classloader:/json-bundler-warbler/bin/run.rb:3
                          load at org/jruby/RubyKernel.java:962
                         <top> at uri:classloader:/META-INF/main.rb:1
                       require at org/jruby/RubyKernel.java:944
                        (root) at uri:classloader:/META-INF/main.rb:1
                         <top> at uri:classloader:/META-INF/jruby.home/lib/ruby/stdlib/rubygems/core_ext/kernel_require.rb:1
ERROR: org.jruby.embed.EvalFailedException: (LoadError) no such file to load -- bundler/dep_proxy

I just stumbled onto this after spending a few hours with a similar issue. Have you found a way to resole this?

http://stackoverflow.com/questions/38071575/jruby-warbler-results-in-no-such-file-to-load-bundler-dep-proxy