InvalidPluginException: Cannot find main class `path.to.MainClass` when Packager is enabled

[Skwrr]

Bug Report

Expected Behaviour

Run the plugin as normal, like if packager weren't enabled

Actual Behaviour

When the obfuscated plugin with packager loads, it throws

Could not load 'plugins\vBases-obf.jar' in folder 'plugins'
org.bukkit.plugin.InvalidPluginException: Cannot find main class `me.skwrr.vbases.vBases'
        at org.bukkit.plugin.java.PluginClassLoader.<init>(PluginClassLoader.java:65) ~[server.jar:1.8.8-R0.2-SNAPSHOT]
        at org.bukkit.plugin.java.JavaPluginLoader.loadPlugin(JavaPluginLoader.java:113) ~[server.jar:1.8.8-R0.2-SNAPSHOT]
        at org.bukkit.plugin.SimplePluginManager.loadPlugin(SimplePluginManager.java:314) ~[server.jar:1.8.8-R0.2-SNAPSHOT]
        at org.bukkit.plugin.SimplePluginManager.loadPlugins(SimplePluginManager.java:232) ~[server.jar:1.8.8-R0.2-SNAPSHOT]
        at org.bukkit.craftbukkit.v1_8_R3.CraftServer.loadPlugins(CraftServer.java:311) ~[server.jar:1.8.8-R0.2-SNAPSHOT]
        at net.minecraft.server.v1_8_R3.DedicatedServer.init(Unknown Source) ~[server.jar:1.8.8-R0.2-SNAPSHOT]
        at net.minecraft.server.v1_8_R3.MinecraftServer.run(Unknown Source) ~[server.jar:1.8.8-R0.2-SNAPSHOT]
        at java.lang.Thread.run(Unknown Source) ~[?:1.8.0_381]
Caused by: java.lang.ClassNotFoundException: me.skwrr.vbases.vBases
        at java.net.URLClassLoader.findClass(Unknown Source) ~[?:1.8.0_381]
        at org.bukkit.plugin.java.PluginClassLoader.findClass(PluginClassLoader.java:100) ~[server.jar:1.8.8-R0.2-SNAPSHOT]
        at org.bukkit.plugin.java.PluginClassLoader.findClass(PluginClassLoader.java:85) ~[server.jar:1.8.8-R0.2-SNAPSHOT]
        at java.lang.ClassLoader.loadClass(Unknown Source) ~[?:1.8.0_381]
        at java.lang.ClassLoader.loadClass(Unknown Source) ~[?:1.8.0_381]
        at java.lang.Class.forName0(Native Method) ~[?:1.8.0_381]
        at java.lang.Class.forName(Unknown Source) ~[?:1.8.0_381]
        at org.bukkit.plugin.java.PluginClassLoader.<init>(PluginClassLoader.java:63) ~[server.jar:1.8.8-R0.2-SNAPSHOT]
        ... 7 more

How to reproduce the behaviour

Load this file as config (change the input jar, output jar and libraries) https://www.mediafire.com/file/qvyq4aobpt2eb5n/Config.jocfg/file
Obfuscate and it will success
Use it in a minecraft server and it will throw that error