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/secure_context.c

@@ -30,7 +30,7 @@ int server_secure_context_free(ServerSecureContext *ctx)
 }
 
 int server_secure_context_add_certificate(ServerSecureContext *ctx,
-    String domain, String cert_file)
+    HTTP_String domain, HTTP_String cert_file, HTTP_String key_file)
 {
     // TODO
 }