use new Filepath functions in more places

src/kernel_internals/runtime/machdep.ml

src/kernel_services/ast_queries/file.ml

src/kernel_services/ast_queries/json_compilation_database.ml

src/kernel_services/plugin_entry_points/plugin.ml

src/libraries/stdlib/extlib.ml

src/libraries/stdlib/extlib.mli

src/libraries/utils/command.ml

src/libraries/utils/command.mli

src/libraries/utils/filepath.mli

src/libraries/utils/json.mli

src/libraries/utils/json.mll

src/plugins/aorai/aorai_register.ml

src/plugins/api-generator/api_generator.ml

src/plugins/markdown-report/md_gen.ml

src/plugins/markdown-report/sarif_gen.ml

src/plugins/report/classify.ml

src/plugins/server/server_doc.ml

src/plugins/wp/Cache.ml

src/plugins/wp/ProofSession.ml

src/plugins/wp/ProofSession.mli