git add alias for git annex that excludes selected file extensions from master and adds them to annex.

gistfile1.sh

#######################
# Setup
#######################
mkdir annex-test
cd annex-test
git init
git annex init master

#######################
# Fab setup task
#######################
git config --local core.excludesfile ./.gitignore_large_binaries
git config --local alias.a '! sh ./git-add.sh'

#######################
# git a (git-add.sh)
#######################

# Generate annex include arg from .gitignore_large_binaries
include_str="--include='.lazy'";

while read line
do
    if [[ "$line" != *"#"* ]] && [[ "$line" != "" ]]; then 
        include_str="$include_str --or --include=${line}";
    fi
done < "./.gitignore_large_binaries"

# git annex add
git config --local core.excludesfile ./.gitignore;
git annex add $1 $include_str;

# git add
git config --local core.excludesfile ./.gitignore_large_binaries;
git add $1

There is support for something like this in newer versions of git-annex.
See: https://git-annex.branchable.com/tips/largefiles/