Multiple broken makefile targets

[jdknives]

Describe the bug
There are two targets that I consider broken in the Makefile right now:

1. Make clean does not use -r flag when removing the build directory and consequently fails. It also fails to remove the ./local directory which we previously used to include. Reasonably so. Unless something about the files contained in local changed, they should also be removed.

2. We have two make build targets while there should be only one. The skywire-cli does not work with defaults of makefile build if we invoke skywire-cli vpn list

3. Is a trivial fix.

4. Requires to update the Makefile and skywire-cli to deal properly with new build paths for apps and other binaries.

Steps to Reproduce

1. Can be reproduced by running make clean after make build && make install
2. Is a little more subtle. Setting up a visor with make build && make install, skywire-cli config gen and then running with ./build/skywire-visor -c skywire-config.json, followed by skywire-cli vpn list will lead to an error because the config has not been generated with the correct apps paths.