The generated dir file is really just an informative file that will show you which directives are used when building the project using Visual Studio. You can use this .dir file anyway that you see fit but it is really not meant to be used as is when building from the command line.
If you wish to use all project settings then the best way to build your application from the command line is to use the msbuild.exe utility from Microsoft that is provided as part of Visual Studio.
If you have a full version of Visual Studio installed then you can open up a Visual Studio Developer command prompt from the Visual Studio-->Tools group under the Start menu and navigate to your project folder and run:
msbuild projname.cblproj
or
msbuild solname.sln
or msbuild
and it will automatically build your project or solution using the specified file name. If you run msbuild without a file name it will search for a file with the .sln extension and build it.
If you are using the Visual Studio shell then you won't have a Visual Studio command prompt and then you just need to add the full path name to the msbuild command when running it from a Visual COBOL command prompt:
The msbuild.exe is part of the .NET Framework and can be located here.
C:\Windows\Microsoft.NET\Framework\v4.0.30319\msbuild.exe
Currently only the 32-bit version of msbuild is supported.