Te copio un manifest que usa librerias, a ver si sacas algo, no he modificado nunca ninguno.
Donde pone name son las librerías, así que creo que no las tienes ahí, ya no se como se pondrían.Código:Manifest-Version: 1.0 Created-By: Fat Jar Eclipse Plug-In Main-Class: cliente.gui.JFLogin Name: junit/framework/TestSuite.class SHA1-Digest: CGdsP9nr3PMH3x7WJVfgqtdg1es= Name: junit/swingui/TestRunner$8.class SHA1-Digest: Vztm0cYdAcLbsK0NklisztX1hGg= Name: junit/awtui/TestRunner$7.class SHA1-Digest: z8q13ze0pKjpmXCsH68oxhPqp0I= Name: junit/swingui/TestRunner$4.class SHA1-Digest: Azk1Xk/plzj5oAVKMiPj3IfSMSk= Name: junit/runner/Sorter$Swapper.class SHA1-Digest: Amtk1k0PmWI8s+mU74GyJOde9fg= Name: junit/awtui/TestRunner$3.class SHA1-Digest: Gxp969OyJajEkDlaMCrz5QVwh1A= Name: junit/swingui/TestRunner$19.class SHA1-Digest: 2aH6gt/nSmAJkXKWz9ydMfOeWBs= Name: junit/framework/ComparisonCompactor.class SHA1-Digest: VBdoWYQx1irQoWwPdIFlZA+3mGM= Name: junit/swingui/TestSuitePanel$1.class SHA1-Digest: DDCE9+Op547/8T/SZ+CHxrdvCfI= Name: junit/swingui/TestRunner$15.class SHA1-Digest: 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Mira esto, no es lo mismo pero a lo mejor te sirve.
http://www.planetacodigo.com/foros/viewtopic.php?id=149
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