[kernel] reorganize system config

share/analysis-scripts/list_functions.ml

src/init/toplevel/toplevel_config.ml

src/kernel_internals/runtime/dump_config.ml

src/kernel_internals/runtime/special_hooks.ml

src/kernel_internals/runtime/system_config.ml.in

src/kernel_internals/runtime/system_config.mli

src/kernel_internals/typing/cabs2cil.ml

src/kernel_services/ast_queries/cil_builtins.ml

src/kernel_services/ast_queries/file.ml

src/kernel_services/cmdline_parameters/cmdline.ml

src/kernel_services/plugin_entry_points/plugin.ml

src/libraries/project/project.ml

src/plugins/eva/domains/cvalue/builtins.ml

src/plugins/eva/utils/library_functions.ml

src/plugins/gui/design.ml

src/plugins/gui/filetree.ml

src/plugins/gui/gtk_helper.ml

src/plugins/gui/help_manager.ml

src/plugins/markdown-report/sarif_gen.ml

src/plugins/server/kernel_main.ml