moved things under Applications

content/Applications/Application_Specific_Guides/Jupyter.md

...Specific_Guides/allinea_profiling_and_debugging/_index.md

...iling_and_debugging/allinea_performance_reports/_index.md

...ormance_reports/blast_with_allinea_performance_reports.md

...rmance_reports/lammps_with_allinea_performance_reports.md

...rformance_reports/ray_with_allinea_performance_reports.md

..._and_debugging/using_allinea_forge_via_reverse_connect.md

...pplication_Specific_Guides/bioinformatics_tools/_index.md

...fic_Guides/bioinformatics_tools/alignment_tools/_index.md

...ides/bioinformatics_tools/alignment_tools/blast/_index.md

...ools/alignment_tools/blast/create_local_blast_database.md

...cs_tools/alignment_tools/blast/running_blast_alignment.md

...cific_Guides/bioinformatics_tools/alignment_tools/blat.md

...fic_Guides/bioinformatics_tools/alignment_tools/bowtie.md

...ic_Guides/bioinformatics_tools/alignment_tools/bowtie2.md

...Guides/bioinformatics_tools/alignment_tools/bwa/_index.md

...rmatics_tools/alignment_tools/bwa/running_bwa_commands.md

...des/bioinformatics_tools/alignment_tools/clustal_omega.md

...es/bioinformatics_tools/alignment_tools/tophat_tophat2.md

...on_Specific_Guides/bioinformatics_tools/biodata_module.md