Restructuring tools and scripts section in the manual:  * merged scripts into tools list  * reordered the list alphabetically  * removed "scripts/" and ".py" from all script commands  * removed description of pod.py script  * fixing typos
Restructuring tools and scripts section in the manual:
 * merged scripts into tools list
 * reordered the list alphabetically
 * removed "scripts/" and ".py" from all script commands
 * removed description of pod.py script
 * fixing typos

jjo31/ATHAM-Fluidity,jrper/fluidity,iakovos-panourgias/fluidity,jrper/fluidity,iakovos-panourgias/fluidity,jrper/fluidity,iakovos-panourgias/fluidity,jrper/fluidity,jjo31/ATHAM-Fluidity,jrper/fluidity,rjferrier/fluidity,rjferrier/fluidity,rjferrier/fluidity,rjferrier/fluidity,jjo31/ATHAM-Fluidity,jjo31/ATHAM-Fluidity,iakovos-panourgias/fluidity,rjferrier/fluidity,iakovos-panourgias/fluidity,jjo31/ATHAM-Fluidity