The compile_commands.json database is used by clangd to understand the
compilation settings of the project. Keep this up to date by making
ninja update it as part of the build, and have it depend on all build
and module files.
This change moves Bonnibel from a separate project into the jsix tree,
and alters the project configuration to be jsix-specific. (I stopped
using bonnibel for any other projects, so it's far easier to make it a
custom generator for jsix.) The build system now also uses actual python
code in `*.module` files to configure modules instead of TOML files.
Target configs (boot, kernel-mode, user-mode) now moved to separate TOML
files under `configs/` and can inherit from one another.
