1. add set nofixendofline into vimrc
2. :e ~/.vimrc
3. :verbose set fixendofline

It should display

nofixendofline
   Last set from ~/.vimrc

But

fixendofline
   Last set from ~/.vimrc

Below is a patch to fix this.

diff --git a/src/buffer.c b/src/buffer.c
index 4623e0a..5d4170f 100644
--- a/src/buffer.c
+++ b/src/buffer.c
@@ -547,7 +547,6 @@ buf_clear_file(buf)
     buf->b_shortname = FALSE;
 #endif
     buf->b_p_eol = TRUE;
-    buf->b_p_fixeol = TRUE;
     buf->b_start_eol = TRUE;
 #ifdef FEAT_MBYTE
     buf->b_p_bomb = FALSE;

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