This is a description of how I think Netbeans could be enhanced:

I edit a file "index.php" from one terminal and upload it to the server.

Later on I am working from another terminal and I need to make some
different changes to index.php but at this second terminal an older
version of index.php is stored locally.

When I try to edit/open index.php, Netbeans warns me that the
remote/FTP version is either newer or different (it checks and compares
file size and modified dates) and do I wish to download it / overwrite the
local version first. I chose to download the version from the FTP server
and edit this one.

At this sage, both me and NB know we are working on the latest version of
index.php so NB doesn't need to ask me if I want to upload the saved
version (and anyway there is a setting in 'options' where I can chose
whether or not I am notified each time NB wants to upload changes).

There is no need to have a function to merge the changes - just a way of reliably checking that you are working on the latest version.

Not an issue that affects me but a potential problem is when two developers are trying to edit the same file simultaneously. Dreamweaver avoids this by having a file 'check in' - 'check out' system - It does this by making the remote files read only when you start editing them and then making the remote files writeable again once you have uploaded and declared that you are finished editing. If another developer using Netbeans tries to edit this file it would discover it is 'read only' and warns the new developer that the file is being edited elsewhere.