Status indexed updates

This PR merges PR #1598 (indexed access to status) and PR #1629 (test for index on case-insensitive file system) plus rebases them on top of the current development branch. This also includes a fix for issue #1649.

On top of those two PRs, this includes fixes for the issues raised in #1629, which in turn makes it easier to address some of the remaining shortcomings of #1598.

This PR is not ready to merge - although it fixes some of the outstanding issues, like #1598, it still needs more tests of case-changing renames and related status cases.

- [x] Pull in relevant PRs
- [x] Fix failing tests / known issues
- [ ] More tests for case-changing renames