NBISweden/AGAT: AGAT-v0.5.0

Fix #49 #50 #51 #54 #55 #58 #60 #62 #63 #64 #65 #66 #67 #68 Merge PR #61

• add new script: agat_sp_flag_premature_stop_codons.pl agat_sp_filter_feature_from_kill_list.pl agat_sp_prokka_fix_fragmented_gene_annotations.pl
• add new parameter --cp to agat_sp_manage_attributes.pl
• update and modify features_level1.json,features_level2.json,features_level3.json files
• locus tag attribute provided by the user now overwritte the default list instead to be appended
• add test 36 in gff_syntax
• add tests for new scripts
• new attachedL2Sequential hash to keep track of the link between l2 and l1 features when sequential.
• fix typo