Add stub directory-level documentation for most source directories

This includes app, core, feature, lib, and tools, but excludes
ext, test, and trunnel.

This was generated by the following shell script:

cd src
for dname in $(find lib core feature app tools -type d |grep -v \\.deps$); do
    keyword="$(echo "$dname" |sed -e "s/\//_/" )"
    target="${dname}/${keyword}.dox"
    echo "$target"
    cat <<EOF >"$target"
/**
@dir ${dname}
@brief ${dname}
**/
EOF

    git add "$target"
done