[plugin manager] Unused plugins aren't removed from the `local_gems` or the bundle's gems directory.

```
# find logstash-2.4.1 -name 'kafka.rb'
logstash-2.4.1/vendor/bundle/jruby/1.9/gems/logstash-input-kafka-2.0.9/lib/logstash/inputs/kafka.rb
logstash-2.4.1/vendor/bundle/jruby/1.9/gems/logstash-output-kafka-2.0.5/lib/logstash/outputs/kafka.rb
logstash-2.4.1/vendor/local_gems/facb65f6/logstash-input-kafka-5.1.0/lib/logstash/inputs/kafka.rb
logstash-2.4.1/vendor/local_gems/78d8d5c6/logstash-output-kafka-5.1.1/lib/logstash/outputs/kafka.rb
logstash-2.4.1/vendor/local_gems/fe38c577/logstash-input-kafka-5.1.0/lib/logstash/inputs/kafka.rb
logstash-2.4.1/vendor/local_gems/92fa9e22/logstash-output-kafka-5.1.1/lib/logstash/outputs/kafka.rb
logstash-2.4.1/vendor/local_gems/9ba87163/logstash-input-kafka-5.1.0/lib/logstash/inputs/kafka.rb
logstash-2.4.1/vendor/local_gems/3f6473d0/logstash-output-kafka-5.1.1/lib/logstash/outputs/kafka.rb
```

For all general issues, please provide the following details for fast resolution:

- Version: 2.4.1
- Operating System: RHEL7
- Steps to Reproduce:
Run multiple times:
```
logstash-plugin install --no-verify --local /tmp/logstash-input-kafka-5.1.0.gem
```
This command was idempotent in Logstash 2.3