Could not find or load main class org.elasticsearch.plugins.PluginManagerCliParser

I am trying to upgrade ES from 2.0.1 to 5.5.1, elasticsearch-5.5.1.jar giving follow error:
Could not find or load main class org.elasticsearch.plugins.PluginManagerCliParser

What is the proper way to upgrade ES from 2.0.1 to 5.5.1?
I am simply replacing lib folder jars into existing one, because our application has custom ssl plugins and infrastructure stuff.

The lib directory is not sufficient. You should remove your existing installation, and install a fresh copy of the new elasticsearch version. In this case, it seems you are still using the old bin scripts.

I compared the bin folder and patch in the differences, now bin/plugin uses PluginManagerCliParser, so this error is resolved.

Now next hurdle, What does this exception mean:

Exception in thread "main" java.lang.NoSuchFieldError: LUCENE_5_3_1
at org.elasticsearch.Version.(Version.java:51)
at org.elasticsearch.common.io.stream.StreamOutput.(StreamOutput.java:74)
at org.elasticsearch.common.io.stream.BytesStream.(BytesStream.java:24)
at org.elasticsearch.common.io.stream.BytesStreamOutput.(BytesStreamOutput.java:59)
at org.elasticsearch.common.io.stream.BytesStreamOutput.(BytesStreamOutput.java:56)
at org.elasticsearch.common.io.stream.BytesStreamOutput.(BytesStreamOutput.java:46)
at org.elasticsearch.common.xcontent.XContentBuilder.builder(XContentBuilder.java:69)
at org.elasticsearch.common.settings.Setting.arrayToParsableString(Setting.java:868)
at org.elasticsearch.common.settings.Setting.lambda$listSetting$29(Setting.java:814)
at org.elasticsearch.common.settings.Setting$2.getRaw(Setting.java:818)
at org.elasticsearch.common.settings.Setting.lambda$listSetting$27(Setting.java:802)
at org.elasticsearch.common.settings.Setting.listSetting(Setting.java:807)
at org.elasticsearch.common.settings.Setting.listSetting(Setting.java:802)
at org.elasticsearch.env.Environment.(Environment.java:60)
at org.elasticsearch.node.InternalSettingsPreparer.prepareEnvironment(InternalSettingsPreparer.java:90)
at org.elasticsearch.cli.EnvironmentAwareCommand.createEnv(EnvironmentAwareCommand.java:72)
at org.elasticsearch.cli.EnvironmentAwareCommand.execute(EnvironmentAwareCommand.java:67)
at org.elasticsearch.cli.Command.mainWithoutErrorHandling(Command.java:122)
at org.elasticsearch.cli.MultiCommand.execute(MultiCommand.java:69)
at org.elasticsearch.cli.Command.mainWithoutErrorHandling(Command.java:122)
at org.elasticsearch.cli.Command.main(Command.java:88)
at org.elasticsearch.plugins.PluginCli.main(PluginCli.java:47)

After removing old lucene jar, only keep new lucene jar from 5.5.1, the above exception is gone.

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