bundler clean is broken

our strategy for purging uninstalled or unused plugins with either

``` ruby
LogStash::Bundler.invoke!(:install => true, :clean => true)
```

or

``` ruby
LogStash::Bundler.invoke!(:update => plugins)
LogStash::Bundler.invoke!(:clean => true)
```

does not work.

the dual `invoke` calls as shown above should work but does not because there is some stale context/state in bundler. in fact, if calling `LogStash::Bundler.invoke!(:clean => true)` from a fresh process, works as shown by @purbon in #3731

relates to #3678 #3731