the following files are 'touched' during a build session

graphics/floor_tiles/atlas.txt
graphics/floor_tiles/floor_tiles_atlas2.png
graphics/obstacles/atlas.txt
graphics/obstacles/obstacles_atlas1.png
graphics/obstacles/obstacles_atlas2.png
graphics/obstacles/obstacles_atlas3.png

after a build, git status shows these files as being modifed.
(ordering of items and the items values are modified)

This interferes with process for making patches (have to exclude these items
specifically or
git checkout -- {each file} 

Is there not a way to have a reference file under git control and write changes
to a game file NOT under git control?

Attached file - git diff between origin/master and clean post-build

so if you   git clean -dfx ; git reset --hard HEAD ; ./autogen.sh ; ./configure
; make ,  these files are modified?

hhhmmmm
scrubbing sources resolves the issue...
hhhmmmm

Marking this as "Works For Me"
After scrubbing sources (git clean), the problem did not reoccur.
Issue might be related to some residual config file in the local repo.

Thx to matthiaskrgr for working with me on this issue. :)

What was tried...
git clean -dfx; git reset --hard HEAD; ./autogen.sh; ./configure; make
result: no issues - git diff shows no changes in files

git clean -dfx; git reset --hard HEAD; ./autogen.sh; ./configure; make -j6
(have bulldozer 6-core cpu)
result: make fails complaining about erros in building gmo files
errors...
----------
mv: cannot stat ‘t-de.gmo’: No such file or directory
Makefile:209: recipe for target 'de.gmo' failed
make[4]: *** [de.gmo] Error 1
make[4]: Leaving directory
'/home/me/localbuild/SRCs/freedroid/freedroid-code/po/po-dialogs'
Makefile:246: recipe for target 'stamp-po' failed
make[3]: *** [stamp-po] Error 2
make[3]: *** Waiting for unfinished jobs....
make[4]: Entering directory
'/home/me/localbuild/SRCs/freedroid/freedroid-code/po/po-dialogs'
installing fr.gmo as ../../locale/fr/LC_MESSAGES/freedroidrpg-dialogs.mo
installing de.gmo as ../../locale/de/LC_MESSAGES/freedroidrpg-dialogs.mo
make[4]: Leaving directory
'/home/me/localbuild/SRCs/freedroid/freedroid-code/po/po-dialogs'
touch stamp-li
make[3]: Leaving directory
'/home/me/localbuild/SRCs/freedroid/freedroid-code/po/po-dialogs'
Makefile:385: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/home/me/localbuild/SRCs/freedroid/freedroid-code/po'
Makefile:536: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/me/localbuild/SRCs/freedroid/freedroid-code'
Makefile:432: recipe for target 'all' failed
make: *** [all] Error 2
----------
run make clean; make; git status
---> file changes in graphics/floor_tiles/ and graphics/obstacle files are found

git clean -dfx; git reset --hard HEAD; ./autogen.sh; ./configure; make -j4
result: no issues - git diff shows no changes in files

this error is "repeatable"

usage of make -j# may not be related (but another issue - covered by problems
with gmo builds).

If I run:
make
make clean
make

there will be differences in the files mentioned above.
build output:
----------
Making all in graphics/floor_tiles
make[2]: Entering directory
'/home/me/localbuild/SRCs/freedroid/freedroid-code/graphics/floor_tiles'
make --directory=../../gluem/
make[3]: Entering directory
'/home/me/localbuild/SRCs/freedroid/freedroid-code/gluem'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/me/localbuild/SRCs/freedroid/freedroid-code/gluem'
./../../gluem/make_atlas floor_tiles_atlas 2048 1024 atlas.txt iso_*.png */iso_*.png
Creating atlas in atlas.txt from 257 images.
Atlas 1 created. Last y position is 1022. Atlas size: 8192kB, images size:
7706kB. Packing efficiency is 0.940716.
Atlas 2 created. Last y position is 202. Atlas size: 2048kB, images size:
1187kB. Packing efficiency is 0.579704.
make[2]: Leaving directory
'/home/me/localbuild/SRCs/freedroid/freedroid-code/graphics/floor_tiles'
Making all in graphics/obstacles
make[2]: Entering directory
'/home/me/localbuild/SRCs/freedroid/freedroid-code/graphics/obstacles'
make --directory=../../gluem/
make[3]: Entering directory
'/home/me/localbuild/SRCs/freedroid/freedroid-code/gluem'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/me/localbuild/SRCs/freedroid/freedroid-code/gluem'
./../../gluem/make_atlas obstacles_atlas 2048 2048 atlas.txt iso_*.png */iso_*.png
Creating atlas in atlas.txt from 518 images.
Atlas 1 created. Last y position is 2047. Atlas size: 16384kB, images size:
15352kB. Packing efficiency is 0.937025.
Atlas 2 created. Last y position is 2047. Atlas size: 16384kB, images size:
15714kB. Packing efficiency is 0.959107.
Atlas 3 created. Last y position is 356. Atlas size: 4096kB, images size:
2397kB. Packing efficiency is 0.585208.
make --directory=../../gluem/
make[3]: Entering directory
'/home/me/localbuild/SRCs/freedroid/freedroid-code/gluem'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/me/localbuild/SRCs/freedroid/freedroid-code/gluem'
./../../gluem/make_atlas obstacles_shadows_atlas 2048 2048 shadow_atlas.txt
shadow_*.png # */shadow_*.png
Creating atlas in shadow_atlas.txt from 172 images.
Atlas 1 created. Last y position is 1121. Atlas size: 16384kB, images size:
8174kB. Packing efficiency is 0.498962.
make[2]: Leaving directory
'/home/me/localbuild/SRCs/freedroid/freedroid-code/graphics/obstacles'
----------
again - this is "repeatable"

Issue related to commands "make clean; make;" and is repeatable.

Well, about your 'git checkout' issue you may as well type:
git add */*atlas* ; git checkout -- */*atlas*
The first 'git add' is to avoid errors on git checkout.

About your last problem...

./../../gluem/make_atlas obstacles_atlas 2048 2048 atlas.txt iso_*.png 
*/iso_*.png
Creating atlas in atlas.txt from 518 images.
Atlas 1 created. Last y position is 2047. Atlas size: 16384kB, images size:
15352kB. Packing efficiency is 0.937025.
Atlas 2 created. Last y position is 2047. Atlas size: 16384kB, images size:
15714kB. Packing efficiency is 0.959107.
Atlas 3 created. Last y position is 356. Atlas size: 4096kB, images size:
2397kB. Packing efficiency is 0.585208.

make ran 'make atlas' which rebuilds the atlas files. Therefore, them were 
"modified". (I'm not going to make a 100-pages-long text expalianing make atlas, 
make clean and make, and how them are going to affect the files. :/)

BTW, if you examine carefully your diffs, you'll see that a few tiles were 
switched with another. (eg, iso_complicated_cmm.png and iso_complicated_cmm2.png)

Marking as closed->works for me. Error appears to have been resolved with
changes to git tree.