Compilation database should be generated earlier

[TheRustifyer]

Refactor

The compilation_database (compile_commands.json) is generated (if necessary) at the very end of the process.

Working with Zero I faced several times where I moved around files, and my neovim setup was unaware of the changes, so it was a total mess of errors and warnings raised by the LSP client.

It would be fine that the compilation database was (re)generated after the generate_commands procedure, and even further, to have a dedicated CLI arg that stands for such purpose, which implies to (re)generate the commands and (re)generate the compilation database, so users can update such entity without running full processes.