Portability of the scripts: suggestion #1
Description
Before I attempt to improve the shell scripts, just to help a bit ... Some discussion.
I assume EasyLAT is meant to be a quite portable and maintainable product.
If so, the (critical) shell scripts should be minimal and portable POSIX, to be tested with the dash shell. That seems not that useful in itself though, as EasyLAT is based on the phusion/baseimage-docker docker image, so GNU/Linux Ubuntu is a given.
However, the scripts should then be replaced by small Python 3 programs without much effort, which would allow for quick somewhat more robust solutions to the filesystem handling that you're doing, while abstracting away details. I'm sure Python programs are far better understood by any people working on or with EasyLAT now or later than shell scripts. A choice to invest in replacing the shell scripts would be attractive to anyone involved, wouldn't it? If it's up to me, Lua, or a statically typed, or whatever language could be used as long as it allows for rapid development and maintainability.
Of course there's limited capacity now, I could help with this esp. if we can split up the work in smaller pieces.