Tell git not to merge binary files but to choose

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You could set up a merge drive in a .gitattributes 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.

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