Java Fn SDK Harness skips unprocessed pCollections

Java Sdk Harness used pCollections to keep track of computed consumers here. This is incorrect as consumers are based on pTransforms so pTransforms should be used to keep track of computed consumers.

In case of Flatten, this creates an issue where pTransforms having same input as that to flatten are not executed. This causes 

https://github.com/apache/beam/blob/ff95a82e461bd8319d9733be60e75992ba90cd7c/sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/FlattenTest.java#L316 to fail.