Bugfix to particle defragmentation

[brryan]

PR Summary

There was a bug in the defragmentation routine acting on particle lists. The issue was that empty indices weren't being updated after defragmentation. This PR fixes that.

As an aside: this produced the surprising effect that simulation correctness depended on frequency of simulation output, even when no particle fields were being output. This is because particle defragmentation is called during every output cycle. Not saying we can't do this, just mentioning it because it was unexpected. Shouldn't be a correctness issue if defragmentation actually works :)

PR Checklist

• Code passes cpplint
• New features are documented.
• Adds a test for any bugs fixed. Adds tests for new features.
• Code is formatted
• Changes are summarized in CHANGELOG.md
• Change is breaking (API, behavior, ...)
  • Change is additionally added to CHANGELOG.md in the breaking section
  • PR is marked as breaking
  • Short summary API changes at the top of the PR (plus optionally with an automated update/fix script)
• CI has been triggered on Darwin for performance regression tests.
• Docs build
• (@lanl.gov employees) Update copyright on changed files

[pdmullen]

LGTM! The defrag in outputs happens even when particles aren't being dumped, which is also likely undesirable.

[Yurlungur]

Regarding defragging in output. We don't have to do this. I could make the output machinery not use it. But it was convenient.