catkin clean does not clean cache for extend

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I'm not entirely sure, but there is no "cache for extend" in catkin_tools.

That setting is part of the currently active profile, and is not affected by catkin clean. You'll have to change that using catkin config --no-extend (if you no longer wish to extend another workspace) or catkin config --extend /path/to/the/workspace/to/extend (if you wish to extend a different workspace).

So it seems that catkin clean did not do anything.

I believe catkin clean did exactly what it was supposed to do, but you seem to want it to do something else.

I want my project to use the content of $CMAKE_PREFIX_PATH in the Extending field but I can't make it work. It continues to get the path from some cached memory, which I have no idea where it is located. Any ideas?

If you can't do what you are after using catkin config --extend .. (to update the setting) then please clarify with some more detail what it is you want to do and perhaps we can help you.

Edit:

I want to extend my work space to more the just one other.

That is specifically not supported (at least, not in the way you are trying to do it).

When ever I used catkin config --extend ... I was able to only extend it to one other work space.

Yes, that is expected.

For that reason, I was trying to use the $CMAKE_PREFIX_PATH variable, which included multiple work spaces.

I'm not sure that will work, but note that to extend multiple workspaces, you'll have to layer them on-top of each other. You may already be familiar with it, but the technique is called workspace overlaying.

Workspace C overlays workspace B, which overlays workspace A. The union of all pkgs in workspaces A, B and C will be available after sourcing workspace C's setup.bash.