To create an md5 file from your application type
md5sum myApplication > myApplication.md5
This is then provided with a download of your application, when the user downloads the application and the .md5 file they can check that the application has not been tampered with in two ways
1 They could open the md5 file they downloaded from your server and compare it to the result of running the md5sum command on the application they have just downloaded eg
md5sum myApplication compared to tail myApplication.md5
2 They could type the following line and let the command compare the results for them giving an OK or FAIL eg
md5sum -c myApplication.md5
By typing the md5sum command as above the command knows which application to compare the results to. For example if you removed the application that you downloaded and typed the above command you would get an error saying that the application it is trying to read is missing.