Best way for over the air deployment is by uploading both the .JAD and the .COD files to a web server. Sometimes the .cod file is actually multiple .cod files and you need to extract it using 7-zip or some other zip utility before you can upload it to the web server.

If you want to make a library (not a stand alone application) this can be done easily within Eclipse. If you go to Project -> Properties and click on the Application tab, you can choose to have your application be a "Library" rather than a "CLDC Application". You can use an external library in your current project by going to Project -> Properties -> Project References and adding the library to your references.

The other files are not useful for over the air deployment, I regret that I can't give you the exact details on what they do.