Please install the other PHP thirdparty apps using Tonido's applications section.
They will be installed in the "plugins" directory.
Then please follow the template from the other apps to build your own app so it shows up in Tonido.

I supose i need to remake the Manifest.xml, but how do i get the checksum on the files ?

You can test and develop with the manifest signature.
Once it is ready to go, we will sign the manifest and put it in the app store for people to install.