Refresh creates duplicate patient entries in the Group resource

[brynrhodes]

Describe the bug
Group resource creation duplicates Patient resources in the Group.

To Reproduce
Steps to reproduce the behavior:

1. Run refresh in the ecqm-content-qicore-2025 repository
2. Note that the resulting Group resources duplicate Patient entries

We suspect that this is because the test case folders contain the test data within individual resource files in the folders, as well as the "bundle" files at the root, as a by-product of the bundling process, and note that the actual fix here is to fix the fact that the bundling process shouldn't be leaving these bundled files around, they cause all sorts of problems in other ways as well.

[brynrhodes]

Right, this issue: #269