Fix minor refactoring errors

Minor fixes:
- Add missing includes in src/includes.h (stdbool, string, stdlib, poll, fcntl, errno, netdb, arpa/inet, netinet/in)
- Fix empty Mutex struct in src/thread.h
- Fix String -> HTTP_String typos in 5 source files
- Fix server_secure_context_add_certificate missing key_file parameter

Non-trivial issues remain (see PR description for details)

src/socket.h

@@ -236,7 +236,7 @@ int socket_manager_listen_tls(SocketManager *sm,
 // authenticity.
 // Returns 0 on success, -1 on error.
 int socket_manager_add_certificate(SocketManager *sm,
-    String domain, String cert_file, String key_file);
+    HTTP_String domain, HTTP_String cert_file, HTTP_String key_file);
 
 // When a thread is blocked on a poll() call for
 // descriptors associated to this socket manager,