refactor LTR/TRIM classification to handle all cases where files might not be present; refactoring LTR/TRIM classification to only use classification method once; bug fix for returning TIR classification directory that is needed by the tirage command; bug fix for setting the correct reference to use for masking after TIR classification; modify method for creating combined library to only return the FASTA instead of FASTA and GFF3; modify GFF3 combining method to not take temp GFF3 as an argument;
refactor LTR/TRIM classification to handle all cases where files might not be present;
refactoring LTR/TRIM classification to only use classification method once;
bug fix for returning TIR classification directory that is needed by the tirage command;
bug fix for setting the correct reference to use for masking after TIR classification;
modify method for creating combined library to only return the FASTA instead of FASTA and GFF3;
modify GFF3 combining method to not take temp GFF3 as an argument;

sestaton/tephra,sestaton/tephra,sestaton/tephra