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. :/)