diff --git a/modules/mono/SCsub b/modules/mono/SCsub
index a2df83925ce..f3cf4c9c5d4 100644
--- a/modules/mono/SCsub
+++ b/modules/mono/SCsub
@@ -18,14 +18,20 @@ def make_cs_files_header(src, dst):
         header.write('#include "ustring.h"\n')
         inserted_files = ''
         import os
-        for file in os.listdir(src):
-            if file.endswith('.cs'):
-                with open(os.path.join(src, file), 'rb') as f:
+        latest_mtime = 0
+        for root, _, files in os.walk(src):
+            files = [f for f in files if f.endswith('.cs')]
+            for file in files:
+                filepath = os.path.join(root, file)
+                filepath_src_rel = os.path.relpath(filepath, src)
+                mtime = os.path.getmtime(filepath)
+                latest_mtime = mtime if mtime > latest_mtime else latest_mtime
+                with open(filepath, 'rb') as f:
                     buf = f.read()
                     decomp_size = len(buf)
                     import zlib
                     buf = zlib.compress(buf)
-                    name = os.path.splitext(file)[0]
+                    name = os.path.splitext(os.path.normpath(filepath_src_rel))[0].strip(os.sep).replace(os.sep, '_').replace('.', '_dotto_')
                     header.write('\nstatic const int _cs_' + name + '_compressed_size = ' + str(len(buf)) + ';\n')
                     header.write('static const int _cs_' + name + '_uncompressed_size = ' + str(decomp_size) + ';\n')
                     header.write('static const unsigned char _cs_' + name + '_compressed[] = { ')
@@ -33,18 +39,13 @@ def make_cs_files_header(src, dst):
                         if i > 0:
                             header.write(', ')
                         header.write(byte_to_str(buf[buf_idx]))
-                    inserted_files += '\tr_files.insert("' + file + '", ' \
+                    inserted_files += '\tr_files.insert("' + filepath_src_rel + '", ' \
                                         'CompressedFile(_cs_' + name + '_compressed_size, ' \
                                         '_cs_' + name + '_uncompressed_size, ' \
                                         '_cs_' + name + '_compressed));\n'
                     header.write(' };\n')
-        version_file = os.path.join(src, 'VERSION.txt')
-        with open(version_file, 'r') as content_file:
-            try:
-                glue_version = int(content_file.read()) # make sure the format is valid
-                header.write('\n#define CS_GLUE_VERSION UINT32_C(' + str(glue_version) + ')\n')
-            except ValueError:
-                raise ValueError('Invalid C# glue version in: ' + version_file)
+        glue_version = int(latest_mtime) # The latest modified time will do for now
+        header.write('\n#define CS_GLUE_VERSION UINT32_C(' + str(glue_version) + ')\n')
         header.write('\nstruct CompressedFile\n' '{\n'
             '\tint compressed_size;\n' '\tint uncompressed_size;\n' '\tconst unsigned char* data;\n'
             '\n\tCompressedFile(int p_comp_size, int p_uncomp_size, const unsigned char* p_data)\n'
diff --git a/modules/mono/editor/bindings_generator.cpp b/modules/mono/editor/bindings_generator.cpp
index 76907451e7b..b97bb5e95f9 100644
--- a/modules/mono/editor/bindings_generator.cpp
+++ b/modules/mono/editor/bindings_generator.cpp
@@ -512,6 +512,15 @@ Error BindingsGenerator::generate_cs_core_project(const String &p_output_dir, bo
 		data.resize(file_data.uncompressed_size);
 		Compression::decompress(data.ptrw(), file_data.uncompressed_size, file_data.data, file_data.compressed_size, Compression::MODE_DEFLATE);
 
+		String output_dir = output_file.get_base_dir();
+
+		if (!DirAccess::exists(output_dir)) {
+			DirAccessRef da = DirAccess::create(DirAccess::ACCESS_FILESYSTEM);
+			ERR_FAIL_COND_V(!da, ERR_CANT_CREATE);
+			Error err = da->make_dir_recursive(ProjectSettings::get_singleton()->globalize_path(output_dir));
+			ERR_FAIL_COND_V(err != OK, ERR_CANT_CREATE);
+		}
+
 		FileAccessRef file = FileAccess::open(output_file, FileAccess::WRITE);
 		ERR_FAIL_COND_V(!file, ERR_FILE_CANT_WRITE);
 		file->store_buffer(data.ptr(), data.size());
diff --git a/modules/mono/editor/godotsharp_builds.cpp b/modules/mono/editor/godotsharp_builds.cpp
index b3b259e8519..0fb87344101 100644
--- a/modules/mono/editor/godotsharp_builds.cpp
+++ b/modules/mono/editor/godotsharp_builds.cpp
@@ -210,6 +210,8 @@ bool GodotSharpBuilds::build_api_sln(const String &p_name, const String &p_api_s
 
 	if (!FileAccess::exists(api_assembly_file)) {
 		MonoBuildInfo api_build_info(api_sln_file, p_config);
+		// TODO Replace this global NoWarn with '#pragma warning' directives on generated files,
+		// once we start to actively document manually maintained C# classes
 		api_build_info.custom_props.push_back("NoWarn=1591"); // Ignore missing documentation warnings
 
 		if (!GodotSharpBuilds::get_singleton()->build(api_build_info)) {
diff --git a/modules/mono/glue/cs_files/VERSION.txt b/modules/mono/glue/cs_files/VERSION.txt
deleted file mode 100755
index ec635144f60..00000000000
--- a/modules/mono/glue/cs_files/VERSION.txt
+++ /dev/null
@@ -1 +0,0 @@
-9