OK
I tried some other stuff today and tried to create a test NIOS SBT App from a template..
This seemed to go ok, and violla there was a debug using nios hardware link available..
So I went a looked at the project properties and some aditional sections were now available regarding Nios II Application Properties.
So I went at did a diff on the .project files and noted the following differences between the imported Custom Makefile Project and the one I created as a new one via the Nios II App and bsp from template..
The following entries were present in the <buildSpec> section of the template created one but were missing from my project file.
<buildCommand>
<name>com.altera.sbtgui.project.makefileBuilder</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>com.altera.sbtgui.project.makefileBuilder</name>
<arguments>
</arguments>
</buildCommand>
And yep there were 2 of them... I don't exactly know why.. another bug I guess..??
And toward the end of the file there were these entries added to the <natures> section
<nature>com.altera.sbtgui.project.SBTGUIAppNature</nature>
<nature>com.altera.sbtgui.project.SBTGUIManagedNature</nature>
So I added these entries into my .project file that the SBT's created during the import. restarted the SBT and guess what I now have the debug via nios ii hardware option and the drop down boxes are populated..
So I guess the import feature to bring in a custom makefile project is broken and is not adding in these settings to tell the SBT that hey this is a nios application..
Or something has changed in the way this import expects things to be within the makefile.
We've been using these makefiles since version 8 of quartus and they are based on the altera ones..
As a further test I tried editing my project file again and only included the:
<nature>com.altera.sbtgui.project.SBTGUIAppNature</nature>
line.
This seemed to work without needing the other entries so I guess that is the critical one that is missing when doing the import..
I will see how things go tomorrow on some actual hardware.