Too many scripts corresponding to README.md were not provided in braker3

[oddguyeee]

[KatharinaHoff]

Thank you for pointing out the outdated documentation!

I removed align2hints.pl and startAlign.pl from the README.md file since they are not longer required to run BRAKER. They are a relict of times prior GeneMark-EP and GeneMark-ETP integration. Fixed with 075383e .

The script change_path_in_perl_scripts.pl is also no longer required since the GeneMark team changed the shebang lines of those perl scripts to /usr/bin/env python3. I updated documentation for this in commit ece9e0f .

If for historical reasons you still want to find the scripts align2hints.pl and startAlign, they are still available in GALBA. I disentangled BRAKER and GALBA a while back because it was controversial to include tools other than GeneMark in BRAKER. https://github.com/Gaius-Augustus/GALBA/blob/main/scripts/startAlign.pl https://github.com/Gaius-Augustus/GALBA/blob/main/scripts/aln2hints.pl (name of second script changes, but it has the same functionality, slightly expanded).

[oddguyeee]

@KatharinaHoff ,
Thank you for your promptly update!