Duplicate sample.md documents breaking Git on macOS

[mwhamgenomics]

There are two 'sample.md' files in docs/manual/data-models, one capitalised and one not. As a result, when I check out this repo onto a macOS machine, I get the following:

% git clone https://github.com/opencb/opencga.git
Cloning into 'opencga'...
[...]
Resolving deltas: 100% (141951/141951), done.
warning: the following paths have collided (e.g. case-sensitive paths
on a case-insensitive filesystem) and only one from the same
colliding group is in the working tree:

  'docs/manual/data-models/Sample.md'
  'docs/manual/data-models/sample.md'

Since macOS's filesystem is case-insensitive by default, I'm then stuck with uncommitted changes:

% git status -s
 M docs/manual/data-models/Sample.md
% git checkout docs/manual/data-models/Sample.md
Updated 1 path from the index
% git status -s                                 
 M docs/manual/data-models/sample.md
% git checkout docs/manual/data-models/sample.md
Updated 1 path from the index
% git status -s                                 
 M docs/manual/data-models/Sample.md
% git checkout v2.1.2
error: Your local changes to the following files would be overwritten by checkout:
	docs/manual/data-models/Sample.md
Please commit your changes or stash them before you switch branches.
Aborting

I tried git config core.ignorecase false, but got the same results. This problem might also be happening on Windows 10. Checking out the repo in Linux works as normal, but I notice that the Sample.md file in the GitHub repo does not appear in my checked out clone:

$ git clone https://github.com/opencb/opencga.git
Cloning into 'opencga'...
[...]
$ cd opencga/
$ ls docs/data-models/?ample.md
docs/data-models/sample.md