Going through the code, my understanding was that it could be done by putting in the config:

binaries: [
  "folder-name/myapp-cli"
],

But then I get an error:

Error: ENOENT: no such file or directory, open 'bin/go-ipfs/ipfs'

As it expects that the full folder to be moved to the bin.

Thanks in advance :)

Update: Some notes fro the digging

https://github.com/avh4/binwrap/blob/master/index.js#L8-L10 uses the binary name to check if it is already present on the bin folder

https://github.com/avh4/binwrap/blob/master/install.js#L22 uses the unpacked folder + binary name to find the binary. However, when a binary is one or more levels deep, it fails to find it.

https://github.com/avh4/binwrap/blob/master/bin/binwrap-install#L16 line that needs to be aware if the bin is somewhere else within the directory (or maybe here https://github.com/avh4/binwrap/blob/master/bin/binwrap-install#L16)