Updating things to be Swan and not Crane

...ioinformatics_tools/data_manipulation_tools/sratoolkit.md

...rmatics_tools/reference_based_assembly_tools/cufflinks.md

...tics_tools/removing_detecting_redundant_sequences/cap3.md

...cs_tools/removing_detecting_redundant_sequences/cd_hit.md

content/applications/app_specific/dmtcp_checkpointing.md

content/applications/app_specific/running_gaussian_at_hcc.md

content/applications/app_specific/running_paraview.md

content/applications/app_specific/running_postgres.md

content/applications/app_specific/running_sas.md

content/applications/app_specific/running_theano.md

content/applications/modules/available_software_for_crane.md

content/connecting/_index.md

content/connecting/how_to_setup_x11_forwarding.md

content/connecting/mobaxterm.md

content/connecting/putty.md

content/connecting/terminal.md

content/good_hcc_practices/._index.md.swp

content/good_hcc_practices/_index.md

content/handling_data/data_storage/_index.md

...nt/handling_data/data_storage/data_for_unmc_users_only.md