AiderDesk Improvements

[pcfreak30]

Right now AD seems to only get installed on a per project basis. However AD has a ~/.aider-desk folder and I would expect things to be installed globally. I would like the skills to be installed as well.

[pcfreak30]

Also the AD bash tool call has a timeout argument so the instructions should be updated b/c i often have to force a retry with a very high timeout.