Doh, I managed to paste the same content twice in my previous mail. I'll 
try again, and delete the original in the online forum one for easier 
reading.

<my mail again, this time with correct paste>

I get the same situation on my machine (OS X 10.8.4). Funny thing is that 
there are actually real diffs, not just some EOL conversion stuff. Excerpt:

diff --git a/extra/linux-03.20.00.13/Documentation/IO-mapping.txt 
b/extra/linux-03.20.00.13/Documentation/IO-mapping.txt
index 1b5aa10..473e43b 100644
--- a/extra/linux-03.20.00.13/Documentation/IO-mapping.txt
+++ b/extra/linux-03.20.00.13/Documentation/IO-mapping.txt
@@ -1,208 +1,82 @@
-[ NOTE: The virt_to_bus() and bus_to_virt() functions have been
-       superseded by the functionality provided by the PCI DMA interface
-       (see Documentation/PCI/PCI-DMA-mapping.txt).  They continue
-       to be documented below for historical purposes, but new code
-       must not use them. --davidm 00/12/12 ]
+The io_mapping functions in linux/io-mapping.h provide an abstraction for
+efficiently mapping small regions of an I/O device to the CPU. The initial
+usage is to support the large graphics aperture on 32-bit processors where
+ioremap_wc cannot be used to statically map the entire aperture to the CPU
+as it would consume too much of the kernel address space.

What's even stranger is that I can't get rid of the changes. git checkout . 
has no effect.

I then had a look at what commits these two pieces of contents appear in:

commit fea79c0e219cd5e43193ce2987b496e04758f3e2
Author: Xander Soldaat <xan...@botbench.com>
Date:   Wed Jul 31 14:58:56 2013 -0700

    Additional files, like kernel, uboot and device specific lib/includes

diff --git a/extra/linux-03.20.00.13/Documentation/io-mapping.txt 
b/extra/linux-03.20.00.13/Documentation/io-mapping.txt
new file mode 100644
index 0000000..473e43b
--- /dev/null
+++ b/extra/linux-03.20.00.13/Documentation/io-mapping.txt
@@ -0,0 +1,82 @@
+The io_mapping functions in linux/io-mapping.h provide an abstraction for
+efficiently mapping small regions of an I/O device to the CPU. The initial
+usage is to support the large graphics aperture on 32-bit processors where
+ioremap_wc cannot be used to statically map the entire aperture to the CPU
+as it would consume too much of the kernel address space.

and 

commit fea79c0e219cd5e43193ce2987b496e04758f3e2
Author: Xander Soldaat <xan...@botbench.com>
Date:   Wed Jul 31 14:58:56 2013 -0700

    Additional files, like kernel, uboot and device specific lib/includes

diff --git a/extra/linux-03.20.00.13/Documentation/IO-mapping.txt 
b/extra/linux-03.20.00.13/Documentation/IO-mapping.txt
new file mode 100644
index 0000000..1b5aa10
--- /dev/null
+++ b/extra/linux-03.20.00.13/Documentation/IO-mapping.txt
@@ -0,0 +1,208 @@
+[ NOTE: The virt_to_bus() and bus_to_virt() functions have been
+       superseded by the functionality provided by the PCI DMA interface
+       (see Documentation/PCI/PCI-DMA-mapping.txt).  They continue
+       to be documented below for historical purposes, but new code
+       must not use them. --davidm 00/12/12 ]

The same commit! And in the same file! Or is it really? No, the first file 
has lowercase letters only, while the other one as IO uppercase.

This means that the author has a filesystem that is case-sensitive, while 
ours is not. So effectively, the second file is checked out on top of the 
other (or the other way around).

So either you have to check out the code on a case sensitive file system, 
or the author has to be a bit nicer and not check in files like that :)

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