The automatically generate ant script does not include a custom manifest file if the project uses libraries but does not
define a main class. 

More precisely, it first does include it by executing the -do-jar-with-manifest target, but then overrides this with a
new jar without it by executing the -do-jar-with-libraries-without-manifest target.

Workaround: Define some main class.

Suggested short term solution: Add warning for projects that define ${manifest.file}, use libraries but do not define
${main.class}.