Примерно вот так.
По поводу




то заменит имена пакетов вначале - то есть если был например com.sun.media.jai.Class1, то получится my.cool.app.jai.Class1.

Насчет



надо уточнить. Можно посмотреть тут

http://code.google.com/p/jarjar/wiki/CommandLineDocs

jarjar wikiThe rules file is a text file, one rule per line. Leading and trailing whitespace is ignored. There are three types of rules:

rule <pattern> <result>
zap <pattern>
keep <pattern>
The standard rule (rule) is used to rename classes. All references to the renamed classes will also be updated. If a class name is matched by more than one rule, only the first one will apply.

<pattern> is a class name with optional wildcards. ** will match against any valid class name substring. To match a single package component (by excluding . from the match), a single * may be used instead.

<result> is a class name which can optionally reference the substrings matched by the wildcards. A numbered reference is available for every * or ** in the <pattern>, starting from left to right: @1, @2, etc. A special @0 reference contains the entire matched class name.

The zap rule causes any matched class to be removed from the resulting jar file. All zap rules are processed before renaming rules.

The keep rule marks all matched classes as "roots". If any keep rules are defined all classes which are not reachable from the roots via dependency analysis are discarded when writing the output jar. This is the last step in the process, after renaming and zapping.