Use `binaries.txt` always as index for binaries

Avoid iterating directly on a directory containing the binaries, and
instead use the `binaries.txt` dir, and specify a folder where the
actual elf are stored.

config.sh

 # This file contains the definition of various support variables useful in different scripts
 basepath=$(pwd)
 binaries_file=$basepath/binaries.txt
+binaries_dir=$basepath/binaries/$arch
 matching_script_dir=$basepath/scripting/boundaries-comparison-scripts
 computation_script_dir=$basepath/scripting/computation
 workdir=$basepath/workdir/$arch

scripting/boundaries-comparison-scripts/compare-all.sh

@@ -14,10 +14,10 @@ if [ ! -d $matching_dir ]; then
   mkdir $matching_dir;
 fi
 
-cd $arch
+readarray -t binaries_array < $binaries_file
 
-for filename in *
+for filename in ${binaries_array[@]}
 do
   echo -e "\nAnalyzing binary: $filename"
-  $matching_script_dir/compare-functions.py $ida_json_dir/$filename.stripped.json.ida $revng_json_dir/$filename.ll.isolated.json.revng $filename $matching_dir/$filename $matching_dir/$filename.matching
+  $matching_script_dir/compare-functions.py $ida_json_dir/$filename.stripped.json.ida $revng_json_dir/$filename.ll.isolated.json.revng $binaries_dir/$filename $matching_dir/$filename $matching_dir/$filename.matching
 done;