moved things under Applications

...uides/bioinformatics_tools/pre_processing_tools/scythe.md

...uides/bioinformatics_tools/pre_processing_tools/sickle.md

...s/bioinformatics_tools/pre_processing_tools/tagcleaner.md

...Application_Specific_Guides/bioinformatics_tools/qiime.md

...nformatics_tools/reference_based_assembly_tools/_index.md

...rmatics_tools/reference_based_assembly_tools/cufflinks.md

...cs_tools/removing_detecting_redundant_sequences/_index.md

...tics_tools/removing_detecting_redundant_sequences/cap3.md

...cs_tools/removing_detecting_redundant_sequences/cd_hit.md

...ations/Application_Specific_Guides/dmtcp_checkpointing.md

...lications/Application_Specific_Guides/fortran_c_on_hcc.md

...plications/Application_Specific_Guides/mpi_jobs_on_hcc.md

...ns/Application_Specific_Guides/running_gaussian_at_hcc.md

...ication_Specific_Guides/running_matlab_parallel_server.md

...ecific_Guides/running_ocean_land_atmosphere_model_olam.md

...pplications/Application_Specific_Guides/running_theano.md

...pplications/Using_Modules/available_software_for_crane.md

...pplications/Using_Modules/available_software_for_rhino.md

content/Applications/Using_Modules/module_commands.md

...sing_Your_Own_Software/compiling_an_openmp_application.md