You could set up a merge drive in a .gitattribute
file (only for a given subtree, only for some file types)
See this question for instance (or this one).
# choose the name of the merge driver to be use for all jar files
echo *.jar merge=keepTheir > dirWithJarFiles\.gitattributes
Declare your merge driver in the config of the Git repo:
git config merge.keepTheir.name "always keep their during merge"
git config merge.keepTheir.driver "keepTheir.sh %O %A %B"
or
git config merge.keepMine.name "always keep mine during merge"
git config merge.keepMine.driver "keepMine.sh %O %A %B"
[merge "keepMine"]
name = always keep mine during merge
driver = keepMine.sh %O %A %B
The example I give don't ask you for a choice but will always keep "mine" (or "yours") version when merging.
But you could adapt the script executed by this merge driver to ask you a question, and then apply your choice to all merges.