The main reason for not getting all the benefits you mentioned (including the context menu and the SSH connectivity issues) is that you created a simple Flex project instead of a bound Flex and PHP project. I suggest you to recreate projects by File > New > Flex and PHP Web or Mobile. (two different options).
What I would like to do is this.
In Flash Builder 4.5.1 for PHP I want to create a "Flex and PHP Project"
I want the PHP project to use the Zend server that I have configured on my linux server 192.168.214.212 ip address.
In the flash builder for php, php project I want to be able to create new functions and classes and then as I do this have them uploaded to the linux zend server via ssh.
I also want to be able to "Introspect" the services and have them create the Value Objects in my flex project.
Then when I debug or launch the project I want it to use the services on the linux server.
If you have zend server installed on the same windows pc (localhost) as flash builder for php all of this works automatically, it creates a public folder and also generates the gateway.php file automatically and everything works with out any manual configuration.
The problem I have is that I cant figure out how to change it so that it uses the linux server and I know it's not as easy as just changing the ipaddress of the server and uploading the files to the linux server webroot as I've already tried this and it doesn't work.
I can ping the linux server and access the zend server admin page.
I can get the flash builder php project connected to the server filesystem (via ssh) and have it upload the php as I change them.
The two things that are not working are Introspect and also the gateway.php and amf_config.ini files are not working.