I don't understand this "Developer Connected".
Do you mean "Developer Options"?
So, it takes 1/4 of a second to list ~5000 files (in /system).
And it takes 4 minutes to list ~16,000 files (in /sdcard).
Your system is trying to tell you what's going on.
Are you allowed to run this:
Please quote the message that logcat is trying to say (just a few lines).
You didn't put any (symbolic) links in the big directory, did you?
Can you try stopping the Android system and see if it makes a difference?
Code:
$ stop
$ cd /storage/emulated/0/Calibre_Companion
$ time ls -Rl | wc
$ start
You're not using the SD card, are you?