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 means the kernel now depends on libj6. I've added the macro
definition __j6kernel when building for the kernel target, so I can
remove parts with #ifdefs.
The last commit was a bandaid, but this needed a real fix. Now we create
a .parse_deps.phony file in every module build dir that implicitly
depends on that module's dependencies' .parse_deps.phony files, as well
as order-only depends on any cog-parsed output for that module. This
causes the cog files to get generated first if they never have been, but
still leaves real header dependency tracking to clang's depfile
generation.
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.
