I'm surprised that anything was deleted from your lib directory - that shouldn't happen.
Dependencies are registered in BuildConfig.groovy in your app and in the plugins that work with Grails 1.2 and above. Older plugins will continue to have jars in their lib directories which will be added to the classpath, and you can still do the same. Obviously it's best to use the dependency management if possible so you have just the one copy of the jar in your Ivy cache instead of one for every project on your machine.
You can run grails dependency-report
to generate Ivy reports to see what's managed by Ivy in each environment. These will end up in target/dependency-report and there's no index file, so just open any of the .html files and you can navigate to the others from there, e.g. target/dependency-report/org.grails.internal-{appname}-runtime.html.