build: fix WriteFile and addCSourceFiles not adding LazyPath deps

Adds a missing call to addLazyPathDependenciesOnly in
std.Build.Module.addCSourceFiles.  Also fixes an issue in
std.Build.Step.WriteFile where it wasn't updating all the GeneratedFile
instances for every directory.  To fix the second issue, I removed
all the GeneratedFile instances and now all files/directories reference
the steps main GeneratedFile via sub paths.

lib/std/Build/Module.zig

@@ -484,6 +484,7 @@ pub fn addCSourceFiles(m: *Module, options: AddCSourceFilesOptions) void {
         .flags = b.dupeStrings(options.flags),
     };
     m.link_objects.append(allocator, .{ .c_source_files = c_source_files }) catch @panic("OOM");
+    addLazyPathDependenciesOnly(m, c_source_files.root);
 }
 
 pub fn addCSourceFile(m: *Module, source: CSourceFile) void {