Update to Entromics_1.0.sh

Entromics_1.0.sh is now Entromics_1.1.sh

Updates:
- Now able to chose to run eS and/or eH (Must run both Nicol and Nisa when running eS).
- Able to chose which sequence to start from (verified this for more than 400 sequence, to this point)
- Files no longer named with date, but a fixed number (to aid Clean_Entromics_1.0.sh)

Removed clean_folder application and replaced it with Clean_Entromics_1.0.sh
- Creates a folder with the current date
- Moves all outputted files to this folder
- Changes their names to match the following schema (Name.#.Program.txt) as is the local Entromics applications

How to run Entromics_1.1.sh:

1. Create folder for sequences (mkdir name)
2. Move sequences to this folder (FilaZilla)
3. cd to given folder in PuTTY
4. Copy Entromics_1.1.sh (cp $HOME/Applications/Entromics_1.1.sh $PWD) <-*this will work from any folder, any folder name*
5. Run Entromics_1.1.sh
6. (Clean_Entromics_1.1.sh is copied automatically)