Plugins have access to manifest inputs

[narekhovhannisyan]

Describe the bug
In case if plugin is implemented in a way that it has to modify the input in the execute method, it affects the manifest inputs too.

To Reproduce
Steps to reproduce the behavior:

1. Implement a plugin that mutates the input.
2. Run the if framework
3. See the output manifest file

Expected behavior
Inputs should stay as they were before.

Actual behavior
Inputs are the same as outputs.