https://github.com/10gen/mongo/commit/0f2cfd57b15f1be4a9270041b06446e2125d4348 was committed as part of SERVER-129188.

Part of that change switched to using `git ls-files` when possible, as opposed to always walking the directory tree, to enumerate *.idl file paths.

The trouble with that is that when this script is called in the context of feature_flag_tags_check.sh, the working tree has been overwritten with the base commit's tree via `git apply`ing a `git diff` patch.

This diff -> apply does not update git's index. So, when we ask git "what are all the .idl files?" it gives us a list that includes .idl files that have been added by the test commit (by the "patch" being evaluated by evergreen) and then removed from the working tree by `git apply`.

Then the call to `buildscripts/idl/gen_all_feature_flag_list.py turned-on-by-default` fails because it's trying to read files that no longer exist.

The changes proposed here filter the output of `git ls-files` to contain only .idl files that are still on the file system.

This change cannot be included as part of the PR that it is blocking, because the version of `gen_all_feature_flag_list.py` executed by evergreen is from the base branch tree, not the tree of the patch under test.