[Solved] Avoid adjusting input entries in mixing schemes.

[peikai]

I found that the usage of process_entries() method needs attention. It only returns the entries that have been processed, not always the complete set of adjusted entries. If input entries have contained energy adjustments, they would not be processed again, and even would not be shown in the results that are returned, which might cause missing entries in phase diagrams, when using them to create phase diagrams. I've ever created a PR, but then closed it to avoid changing this usage.

#2830

[peikai]

[Solved] A new inplace flag has been add into process_entries() method in the PR #2841.