Can anyone help me with step by step instructions on how to integrate nucoder to phpED so I can encode single files with a menu or right click option.
My project is quite large and i don't want to encode the whole project each time I make a simple change nor do i want to encode the file on upload.
ie if I have a project file of say mysite/myfolder/myfile.php to be encoded and saved to E:\encoded_files\mysite\myfolder\myfile.php

Can this be done?

many thanks

You can only encode single files from the command line.

you can encode all the scripts in a directory and below with -r option
for example:

nu-coder -c5.1 -r "c:\my dev project" "c:\target dir"

to run this command via integration, just add this command into the intagration (tools->settings->integraion):
Execute with: Shell
Command line: "c:\program files\nusphere\nucoder\nu-coder.exe" -c 5.1 --copyall -r "@FName@" "@FName@.destination"
Show this command in Workspace popup: checked
for directories and projects: checked

all the rest should be left unchecked

By running this command on a directory in the workspace you will create a directory with the same name and .destination appended to the right and all the files and subdirectories. Php files will be encoded, all the other files will be copied as is.
If you have a separate directory you may want to use something like this:
Command line: "c:\program files\nusphere\nucoder\nu-coder.exe" -c 5.1 --copyall -r "@FName@" "c:/separated directory/@RelPath@/"