Git status shows files as changed even though contents are the same

Question

I received a git checkout from someone else and am trying to commit the unstaged changes to the local repository. However, a lot (if not every) file appears as modified even though the contents are exactly the same.

I already set core.fileMode to false and also set core.autocrlf to false, without success.

Worth mentioning is that the Git repo I received was from someone using Windows, while I use Linux.

What can I do to commit the actual changes?

EDIT: output of git config -l:

user.name=Aron Rotteveel
user.email=<removed>
color.diff=auto
color.status=auto
color.branch=auto
color.interactive=auto
color.ui=true
color.pager=true
color.branch.current=yellow reverse
color.branch.local=yellow
color.branch.remote=green
color.diff.meta=yellow bold
color.diff.frag=magenta bold
color.diff.old=red bold
color.diff.new=green bold
color.status.added=yellow
color.status.changed=green
color.status.untracked=cyan
core.pager=less -FRSX
core.whitespace=fix,-indent-with-non-tab,trailing-space,cr-at-eol
alias.co=checkout
core.repositoryformatversion=0
core.filemode=false
core.bare=false
core.logallrefupdates=true
core.symlinks=false
core.ignorecase=true
core.hidedotfiles=dotGitOnly
core.autocrlf=false
remote.origin.url=<removed>
remote.origin.fetch=+refs/heads/*:refs/remotes/origin/*

Update: added some random example files. These files are just plaintext, so are the easiest to include.

Original files are located here: https://gist.github.com/c3c5302430935155ef3d. Hexdumps definately indicate that the files are different, but I have no clue what causes this, and how to fix it.

HEAD version:

0000000: 4854 4d4c 2e53 6166 654f 626a 6563 740d  HTML.SafeObject.
0000010: 0a54 5950 453a 2062 6f6f 6c0d 0a56 4552  .TYPE: bool..VER
0000020: 5349 4f4e 3a20 332e 312e 310d 0a44 4546  SION: 3.1.1..DEF
0000030: 4155 4c54 3a20 6661 6c73 650d 0a2d 2d44  AULT: false..--D
0000040: 4553 4352 4950 5449 4f4e 2d2d 0d0a 3c70  ESCRIPTION--..<p
0000050: 3e0d 0a20 2020 2057 6865 7468 6572 206f  >..    Whether o
0000060: 7220 6e6f 7420 746f 2070 6572 6d69 7420  r not to permit 
0000070: 6f62 6a65 6374 2074 6167 7320 696e 2064  object tags in d
0000080: 6f63 756d 656e 7473 2c20 7769 7468 2061  ocuments, with a
0000090: 206e 756d 6265 7220 6f66 2065 7874 7261   number of extra
00000a0: 0d0a 2020 2020 7365 6375 7269 7479 2066  ..    security f
00000b0: 6561 7475 7265 7320 6164 6465 6420 746f  eatures added to
00000c0: 2070 7265 7665 6e74 2073 6372 6970 7420   prevent script 
00000d0: 6578 6563 7574 696f 6e2e 2054 6869 7320  execution. This 
00000e0: 6973 2073 696d 696c 6172 2074 6f0d 0a20  is similar to.. 
00000f0: 2020 2077 6861 7420 7765 6273 6974 6573     what websites
0000100: 206c 696b 6520 4d79 5370 6163 6520 646f   like MySpace do
0000110: 2074 6f20 6f62 6a65 6374 2074 6167 732e   to object tags.
0000120: 2020 596f 7520 7368 6f75 6c64 2061 6c73    You should als
0000130: 6f20 656e 6162 6c65 0d0a 2020 2020 254f  o enable..    %O
0000140: 7574 7075 742e 466c 6173 6843 6f6d 7061  utput.FlashCompa
0000150: 7420 696e 206f 7264 6572 2074 6f20 6765  t in order to ge
0000160: 6e65 7261 7465 2049 6e74 6572 6e65 7420  nerate Internet 
0000170: 4578 706c 6f72 6572 0d0a 2020 2020 636f  Explorer..    co
0000180: 6d70 6174 6962 696c 6974 7920 636f 6465  mpatibility code
0000190: 2066 6f72 2079 6f75 7220 6f62 6a65 6374   for your object
00001a0: 2074 6167 732e 0d0a 3c2f 703e 0d0a 2d2d   tags...</p>..--
00001b0: 2320 7669 6d3a 2065 7420 7377 3d34 2073  # vim: et sw=4 s
00001c0: 7473 3d34 0d0a                           ts=4..

Copied version:

0000000: 4854 4d4c 2e53 6166 654f 626a 6563 740a  HTML.SafeObject.
0000010: 5459 5045 3a20 626f 6f6c 0a56 4552 5349  TYPE: bool.VERSI
0000020: 4f4e 3a20 332e 312e 310a 4445 4641 554c  ON: 3.1.1.DEFAUL
0000030: 543a 2066 616c 7365 0a2d 2d44 4553 4352  T: false.--DESCR
0000040: 4950 5449 4f4e 2d2d 0a3c 703e 0a20 2020  IPTION--.<p>.   
0000050: 2057 6865 7468 6572 206f 7220 6e6f 7420   Whether or not 
0000060: 746f 2070 6572 6d69 7420 6f62 6a65 6374  to permit object
0000070: 2074 6167 7320 696e 2064 6f63 756d 656e   tags in documen
0000080: 7473 2c20 7769 7468 2061 206e 756d 6265  ts, with a numbe
0000090: 7220 6f66 2065 7874 7261 0a20 2020 2073  r of extra.    s
00000a0: 6563 7572 6974 7920 6665 6174 7572 6573  ecurity features
00000b0: 2061 6464 6564 2074 6f20 7072 6576 656e   added to preven
00000c0: 7420 7363 7269 7074 2065 7865 6375 7469  t script executi
00000d0: 6f6e 2e20 5468 6973 2069 7320 7369 6d69  on. This is simi
00000e0: 6c61 7220 746f 0a20 2020 2077 6861 7420  lar to.    what 
00000f0: 7765 6273 6974 6573 206c 696b 6520 4d79  websites like My
0000100: 5370 6163 6520 646f 2074 6f20 6f62 6a65  Space do to obje
0000110: 6374 2074 6167 732e 2020 596f 7520 7368  ct tags.  You sh
0000120: 6f75 6c64 2061 6c73 6f20 656e 6162 6c65  ould also enable
0000130: 0a20 2020 2025 4f75 7470 7574 2e46 6c61  .    %Output.Fla
0000140: 7368 436f 6d70 6174 2069 6e20 6f72 6465  shCompat in orde
0000150: 7220 746f 2067 656e 6572 6174 6520 496e  r to generate In
0000160: 7465 726e 6574 2045 7870 6c6f 7265 720a  ternet Explorer.
0000170: 2020 2020 636f 6d70 6174 6962 696c 6974      compatibilit
0000180: 7920 636f 6465 2066 6f72 2079 6f75 7220  y code for your 
0000190: 6f62 6a65 6374 2074 6167 732e 0a3c 2f70  object tags..</p
00001a0: 3e0a 2d2d 2320 7669 6d3a 2065 7420 7377  >.--# vim: et sw
00001b0: 3d34 2073 7473 3d34 0a                   =4 sts=4.

Answer 1

I have resolved this problem using following steps

1. Remove every file from Git's index.

   git rm --cached -r .

2. Rewrite the Git index to pick up all the new line endings.

   git reset --hard

Note that step 2 may remove your local changes. Solution was part of steps described on git site https://help.github.com/articles/dealing-with-line-endings/