I just cloned a repo and the first thing it says in Github is "Uncommitted changes"? Not CRLF related

Question

Bear with me I'm completely new to Github but have experience with TortoiseSVN, diffs, adding, committing, etc.

So I just cloned https://github.com/faux123/Nexus_5/ want to poke around.

The first thing I notice looking at the clone on desktop is there are about 10 files with uncommitted changes that I did not make. New content, not just a different line endings...

Why is this, and how do I make it stop?

$ git status
# On branch kk_mr2
# Changes not staged for commit:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#       modified:   include/linux/netfilter/xt_CONNMARK.h
#       modified:   include/linux/netfilter/xt_DSCP.h
#       modified:   include/linux/netfilter/xt_MARK.h
#       modified:   include/linux/netfilter/xt_RATEEST.h
#       modified:   include/linux/netfilter/xt_TCPMSS.h
#       modified:   include/linux/netfilter_ipv4/ipt_ECN.h
#       modified:   include/linux/netfilter_ipv4/ipt_TTL.h
#       modified:   include/linux/netfilter_ipv6/ip6t_HL.h
#       modified:   net/netfilter/xt_DSCP.c
#       modified:   net/netfilter/xt_HL.c
#       modified:   net/netfilter/xt_RATEEST.c
#       modified:   net/netfilter/xt_TCPMSS.c
#
no changes added to commit (use "git add" and/or "git commit -a")

here's an example of one of the files, xt_CONNMARK.h

@@ -1,6 +1,31 @@
-#ifndef _XT_CONNMARK_H_target
-#define _XT_CONNMARK_H_target
+#ifndef _XT_CONNMARK_H
+#define _XT_CONNMARK_H

-#include <linux/netfilter/xt_connmark.h>
+#include <linux/types.h>

-#endif /*_XT_CONNMARK_H_target*/
+/* Copyright (C) 2002,2004 MARA Systems AB <http://www.marasystems.com>
+* by Henrik Nordstrom <hno@marasystems.com>
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ */
+
+enum {
+   XT_CONNMARK_SET = 0,
+   XT_CONNMARK_SAVE,
+   XT_CONNMARK_RESTORE
+};
+
+struct xt_connmark_tginfo1 {
+   __u32 ctmark, ctmask, nfmask;
+   __u8 mode;
+};
+
+struct xt_connmark_mtinfo1 {
+   __u32 mark, mask;
+   __u8 invert;
+};
+
+#endif /*_XT_CONNMARK_H*/

Answer 1

It happens because a a filename case issue.

In include/linux/netfilter, xt_CONNMARK.h exists also as xt_connmark.h, in the same folder.

Windows, as a case insensitive environment, doesn't know how to handle it: the last one override the first.

include/linux/netfilter/xt_CONNMARK.h
include/linux/netfilter/xt_connmark.h

include/linux/netfilter_ipv4/ipt_ECN.h
include/linux/netfilter_ipv4/ipt_ecn.h

It is likely that your core.ignorecase config is set to true, which makes git ignore the issue and override xt_CONNMARK.h with xt_connmark.h.

In other words, this repo isn't meant to be cloned on Windows.